Macarron is a workflow to systematically annotate and prioritize potentially bioactive (and often unannotated) small molecules in microbial community metabolomic datasets. Macarron prioritizes metabolic features as potentially bioactive in a phenotype/condition of interest using a combination of (a) covariance with annotated metabolites, (b) ecological properties such as abundance with respect to covarying annotated compounds, and (c) differential abundance in the phenotype/condition of interest.
If you have questions, please direct it to: Macarron Forum
Macarron requires R version 4.2.0 or higher. Install Bioconductor and then install Macarron:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Macarron")
Macarron can be run from the command line or as an R function. Both methods require the same
arguments, have the same options, and use the same default settings. The package includes the
wrapper Macarron()
as well as functions which perform different steps in the Macarron
framework.
Macarron requires 4 comma-separated, appropriately formatted input files. The files and their formatting constraints are described below.
If you do not have the chemical taxonomy file, you can generate this file using the annotation dataframe and Macarron utility decorate_ID
(see Advanced Topics).
By default, all files will be stored in a folder named Macarron_output inside the current working directory. The main prioritization results are stored in prioritized_metabolites_all.csv
. Another file, prioritized_metabolites_characterizable.csv
is a subset of prioritized_metabolites_all.csv
and only contains metabolic features which covary with at least one annotated metabolite.
The columns in these output files are:
Maaslin2
.Example (demo) input files can be found under inst/extdata
folder of the Macarron
source. These files were generated from the PRISM study of stool metabolomes of individuals with inflammatory bowel disease (IBD) and healthy “Control” individuals. Control and IBD are the two phenotypes in this example. Macarron will be applied to prioritize metabolic features with respect to their bioactivity in IBD. Therefore, in this example, the phenotype of interest is “IBD” and the reference phenotype is “Control”. The four input files are demo_abundances.csv
, demo_annotations.csv
, demo_metadata.csv
, and demo_taxonomy.csv
.
library(Macarron)
## Loading required package: SummarizedExperiment
## Loading required package: MatrixGenerics
## Loading required package: matrixStats
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## Attaching package: 'MatrixGenerics'
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## Welcome to Bioconductor
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prism_abundances <- system.file(
'extdata','demo_abundances.csv', package="Macarron")
prism_annotations <-system.file(
'extdata','demo_annotations.csv', package="Macarron")
prism_metadata <-system.file(
'extdata','demo_metadata.csv', package="Macarron")
mets_taxonomy <-system.file(
'extdata','demo_taxonomy.csv', package="Macarron")
prism_prioritized <- Macarron::Macarron(input_abundances = prism_abundances,
input_annotations = prism_annotations,
input_metadata = prism_metadata,
input_taxonomy = mets_taxonomy)
## 2024-05-01 19:23:34.575887 INFO::Creating output folder.
## 2024-05-01 19:23:34.588993 INFO::Writing function arguments to log file
## Samples with both abundances and metadata: 102
## 2024-05-01 19:23:34.653801 INFO::Summarized Experiment created.
## 2024-05-01 19:23:34.656278 INFO::Metadata chosen for prevalence filtering: diagnosis
## 869 features pass chosen minimum prevalence threshold of 0.7.
## Calculating pairwise correlations in phenotype: IBD
##
## Calculating pairwise correlations in phenotype: Control
## Distance matrix with 869 features created.
## 2024-05-01 19:23:39.943723 INFO::Distance matrix with 869 metabolic features created.
## Initiating module detection
## 2024-05-01 19:23:39.947031 INFO::Minimum module size used for this dataset: 10
## Tree constructed
## Evaluating measures of success
## ..cutHeight not given, setting it to 0.99 ===> 99% of the (truncated) height range in dendro.
## ..done.
## ..cutHeight not given, setting it to 0.99 ===> 99% of the (truncated) height range in dendro.
## ..done.
## ..cutHeight not given, setting it to 0.99 ===> 99% of the (truncated) height range in dendro.
## ..done.
## ..cutHeight not given, setting it to 0.99 ===> 99% of the (truncated) height range in dendro.
## ..done.
## ..cutHeight not given, setting it to 0.99 ===> 99% of the (truncated) height range in dendro.
## ..done.
## 2024-05-01 19:23:42.535026 INFO::Total number of modules detected: 30
## Initiating AVA calculations
## Finding anchors
## Calculating AVA
## Initiating q-value calculations
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2024-05-01 19:23:45.261249 INFO::Writing function arguments to log file
## 2024-05-01 19:23:45.278656 INFO::Verifying options selected are valid
## 2024-05-01 19:23:45.35657 INFO::Determining format of input files
## 2024-05-01 19:23:45.359629 INFO::Input format is data samples as columns and metadata samples as rows
## 2024-05-01 19:23:45.393065 INFO::Formula for fixed effects: expr ~ diagnosis + age + antibiotics
## 2024-05-01 19:23:45.397214 INFO::Filter data based on min abundance and min prevalence
## 2024-05-01 19:23:45.399719 INFO::Total samples in data: 102
## 2024-05-01 19:23:45.402059 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
## 2024-05-01 19:23:45.421176 INFO::Total filtered features: 0
## 2024-05-01 19:23:45.423704 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-05-01 19:23:45.443664 INFO::Total filtered features with variance filtering: 0
## 2024-05-01 19:23:45.446018 INFO::Filtered feature names from variance filtering:
## 2024-05-01 19:23:45.44778 INFO::Running selected normalization method: NONE
## 2024-05-01 19:23:45.449828 INFO::Applying z-score to standardize continuous metadata
## 2024-05-01 19:23:45.474343 INFO::Running selected transform method: NONE
## 2024-05-01 19:23:45.477192 INFO::Running selected analysis method: LM
## 2024-05-01 19:23:45.489911 INFO::Fitting model to feature number 1, F1
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## 2024-05-01 19:23:46.570536 INFO::Fitting model to feature number 185, F191
## 2024-05-01 19:23:46.575724 INFO::Fitting model to feature number 186, F192
## 2024-05-01 19:23:46.580959 INFO::Fitting model to feature number 187, F193
## 2024-05-01 19:23:46.586787 INFO::Fitting model to feature number 188, F194
## 2024-05-01 19:23:46.591874 INFO::Fitting model to feature number 189, F195
## 2024-05-01 19:23:46.596936 INFO::Fitting model to feature number 190, F196
## 2024-05-01 19:23:46.601904 INFO::Fitting model to feature number 191, F197
## 2024-05-01 19:23:46.60692 INFO::Fitting model to feature number 192, F198
## 2024-05-01 19:23:46.611793 INFO::Fitting model to feature number 193, F199
## 2024-05-01 19:23:46.61669 INFO::Fitting model to feature number 194, F200
## 2024-05-01 19:23:46.621656 INFO::Fitting model to feature number 195, F201
## 2024-05-01 19:23:46.626617 INFO::Fitting model to feature number 196, F202
## 2024-05-01 19:23:46.631713 INFO::Fitting model to feature number 197, F203
## 2024-05-01 19:23:46.636835 INFO::Fitting model to feature number 198, F204
## 2024-05-01 19:23:46.641751 INFO::Fitting model to feature number 199, F206
## 2024-05-01 19:23:46.646762 INFO::Fitting model to feature number 200, F207
## 2024-05-01 19:23:46.651715 INFO::Fitting model to feature number 201, F208
## 2024-05-01 19:23:46.656754 INFO::Fitting model to feature number 202, F209
## 2024-05-01 19:23:46.661741 INFO::Fitting model to feature number 203, F210
## 2024-05-01 19:23:46.666726 INFO::Fitting model to feature number 204, F211
## 2024-05-01 19:23:46.67176 INFO::Fitting model to feature number 205, F212
## 2024-05-01 19:23:46.676691 INFO::Fitting model to feature number 206, F213
## 2024-05-01 19:23:46.681952 INFO::Fitting model to feature number 207, F214
## 2024-05-01 19:23:46.686919 INFO::Fitting model to feature number 208, F215
## 2024-05-01 19:23:46.692458 INFO::Fitting model to feature number 209, F216
## 2024-05-01 19:23:46.697458 INFO::Fitting model to feature number 210, F217
## 2024-05-01 19:23:46.703526 INFO::Fitting model to feature number 211, F218
## 2024-05-01 19:23:46.7099 INFO::Fitting model to feature number 212, F219
## 2024-05-01 19:23:46.715122 INFO::Fitting model to feature number 213, F220
## 2024-05-01 19:23:46.720126 INFO::Fitting model to feature number 214, F221
## 2024-05-01 19:23:46.725091 INFO::Fitting model to feature number 215, F222
## 2024-05-01 19:23:46.729995 INFO::Fitting model to feature number 216, F223
## 2024-05-01 19:23:46.735134 INFO::Fitting model to feature number 217, F224
## 2024-05-01 19:23:46.74268 INFO::Fitting model to feature number 218, F225
## 2024-05-01 19:23:46.749917 INFO::Fitting model to feature number 219, F226
## 2024-05-01 19:23:46.757933 INFO::Fitting model to feature number 220, F227
## 2024-05-01 19:23:46.763028 INFO::Fitting model to feature number 221, F228
## 2024-05-01 19:23:46.767921 INFO::Fitting model to feature number 222, F229
## 2024-05-01 19:23:46.772775 INFO::Fitting model to feature number 223, F230
## 2024-05-01 19:23:46.777937 INFO::Fitting model to feature number 224, F231
## 2024-05-01 19:23:46.782843 INFO::Fitting model to feature number 225, F232
## 2024-05-01 19:23:46.787727 INFO::Fitting model to feature number 226, F233
## 2024-05-01 19:23:46.792651 INFO::Fitting model to feature number 227, F234
## 2024-05-01 19:23:46.797511 INFO::Fitting model to feature number 228, F235
## 2024-05-01 19:23:46.802314 INFO::Fitting model to feature number 229, F236
## 2024-05-01 19:23:46.807116 INFO::Fitting model to feature number 230, F237
## 2024-05-01 19:23:46.811963 INFO::Fitting model to feature number 231, F238
## 2024-05-01 19:23:46.81676 INFO::Fitting model to feature number 232, F239
## 2024-05-01 19:23:46.821661 INFO::Fitting model to feature number 233, F240
## 2024-05-01 19:23:46.826509 INFO::Fitting model to feature number 234, F241
## 2024-05-01 19:23:46.831427 INFO::Fitting model to feature number 235, F242
## 2024-05-01 19:23:46.836407 INFO::Fitting model to feature number 236, F243
## 2024-05-01 19:23:46.841425 INFO::Fitting model to feature number 237, F244
## 2024-05-01 19:23:46.846442 INFO::Fitting model to feature number 238, F245
## 2024-05-01 19:23:46.851344 INFO::Fitting model to feature number 239, F246
## 2024-05-01 19:23:46.856422 INFO::Fitting model to feature number 240, F247
## 2024-05-01 19:23:46.861371 INFO::Fitting model to feature number 241, F248
## 2024-05-01 19:23:46.866277 INFO::Fitting model to feature number 242, F249
## 2024-05-01 19:23:46.871182 INFO::Fitting model to feature number 243, F250
## 2024-05-01 19:23:46.876298 INFO::Fitting model to feature number 244, F252
## 2024-05-01 19:23:46.881479 INFO::Fitting model to feature number 245, F253
## 2024-05-01 19:23:46.886489 INFO::Fitting model to feature number 246, F254
## 2024-05-01 19:23:46.89159 INFO::Fitting model to feature number 247, F255
## 2024-05-01 19:23:46.896573 INFO::Fitting model to feature number 248, F256
## 2024-05-01 19:23:46.901759 INFO::Fitting model to feature number 249, F257
## 2024-05-01 19:23:46.906859 INFO::Fitting model to feature number 250, F259
## 2024-05-01 19:23:46.911947 INFO::Fitting model to feature number 251, F260
## 2024-05-01 19:23:46.916997 INFO::Fitting model to feature number 252, F261
## 2024-05-01 19:23:46.922087 INFO::Fitting model to feature number 253, F262
## 2024-05-01 19:23:46.927126 INFO::Fitting model to feature number 254, F263
## 2024-05-01 19:23:46.932191 INFO::Fitting model to feature number 255, F264
## 2024-05-01 19:23:46.937259 INFO::Fitting model to feature number 256, F265
## 2024-05-01 19:23:46.942748 INFO::Fitting model to feature number 257, F266
## 2024-05-01 19:23:46.949033 INFO::Fitting model to feature number 258, F267
## 2024-05-01 19:23:46.989561 INFO::Fitting model to feature number 259, F269
## 2024-05-01 19:23:46.994851 INFO::Fitting model to feature number 260, F270
## 2024-05-01 19:23:47.001315 INFO::Fitting model to feature number 261, F271
## 2024-05-01 19:23:47.009264 INFO::Fitting model to feature number 262, F272
## 2024-05-01 19:23:47.016667 INFO::Fitting model to feature number 263, F273
## 2024-05-01 19:23:47.024425 INFO::Fitting model to feature number 264, F274
## 2024-05-01 19:23:47.03222 INFO::Fitting model to feature number 265, F276
## 2024-05-01 19:23:47.040094 INFO::Fitting model to feature number 266, F277
## 2024-05-01 19:23:47.047942 INFO::Fitting model to feature number 267, F278
## 2024-05-01 19:23:47.055588 INFO::Fitting model to feature number 268, F279
## 2024-05-01 19:23:47.06318 INFO::Fitting model to feature number 269, F280
## 2024-05-01 19:23:47.070993 INFO::Fitting model to feature number 270, F281
## 2024-05-01 19:23:47.078927 INFO::Fitting model to feature number 271, F282
## 2024-05-01 19:23:47.086719 INFO::Fitting model to feature number 272, F283
## 2024-05-01 19:23:47.09468 INFO::Fitting model to feature number 273, F284
## 2024-05-01 19:23:47.10253 INFO::Fitting model to feature number 274, F285
## 2024-05-01 19:23:47.110185 INFO::Fitting model to feature number 275, F286
## 2024-05-01 19:23:47.117717 INFO::Fitting model to feature number 276, F287
## 2024-05-01 19:23:47.125303 INFO::Fitting model to feature number 277, F288
## 2024-05-01 19:23:47.132691 INFO::Fitting model to feature number 278, F289
## 2024-05-01 19:23:47.140232 INFO::Fitting model to feature number 279, F290
## 2024-05-01 19:23:47.147913 INFO::Fitting model to feature number 280, F292
## 2024-05-01 19:23:47.155647 INFO::Fitting model to feature number 281, F293
## 2024-05-01 19:23:47.163139 INFO::Fitting model to feature number 282, F294
## 2024-05-01 19:23:47.170541 INFO::Fitting model to feature number 283, F295
## 2024-05-01 19:23:47.178392 INFO::Fitting model to feature number 284, F296
## 2024-05-01 19:23:47.18624 INFO::Fitting model to feature number 285, F297
## 2024-05-01 19:23:47.193268 INFO::Fitting model to feature number 286, F298
## 2024-05-01 19:23:47.198439 INFO::Fitting model to feature number 287, F299
## 2024-05-01 19:23:47.203275 INFO::Fitting model to feature number 288, F300
## 2024-05-01 19:23:47.208066 INFO::Fitting model to feature number 289, F301
## 2024-05-01 19:23:47.213809 INFO::Fitting model to feature number 290, F302
## 2024-05-01 19:23:47.221212 INFO::Fitting model to feature number 291, F303
## 2024-05-01 19:23:47.228861 INFO::Fitting model to feature number 292, F304
## 2024-05-01 19:23:47.236413 INFO::Fitting model to feature number 293, F305
## 2024-05-01 19:23:47.243992 INFO::Fitting model to feature number 294, F306
## 2024-05-01 19:23:47.25113 INFO::Fitting model to feature number 295, F307
## 2024-05-01 19:23:47.258227 INFO::Fitting model to feature number 296, F308
## 2024-05-01 19:23:47.265688 INFO::Fitting model to feature number 297, F309
## 2024-05-01 19:23:47.272901 INFO::Fitting model to feature number 298, F310
## 2024-05-01 19:23:47.280335 INFO::Fitting model to feature number 299, F311
## 2024-05-01 19:23:47.287885 INFO::Fitting model to feature number 300, F312
## 2024-05-01 19:23:47.295537 INFO::Fitting model to feature number 301, F313
## 2024-05-01 19:23:47.303066 INFO::Fitting model to feature number 302, F315
## 2024-05-01 19:23:47.310763 INFO::Fitting model to feature number 303, F316
## 2024-05-01 19:23:47.318369 INFO::Fitting model to feature number 304, F317
## 2024-05-01 19:23:47.325955 INFO::Fitting model to feature number 305, F318
## 2024-05-01 19:23:47.339425 INFO::Fitting model to feature number 306, F319
## 2024-05-01 19:23:47.34706 INFO::Fitting model to feature number 307, F320
## 2024-05-01 19:23:47.354564 INFO::Fitting model to feature number 308, F321
## 2024-05-01 19:23:47.36219 INFO::Fitting model to feature number 309, F322
## 2024-05-01 19:23:47.369614 INFO::Fitting model to feature number 310, F323
## 2024-05-01 19:23:47.375757 INFO::Fitting model to feature number 311, F324
## 2024-05-01 19:23:47.38096 INFO::Fitting model to feature number 312, F325
## 2024-05-01 19:23:47.385803 INFO::Fitting model to feature number 313, F326
## 2024-05-01 19:23:47.391357 INFO::Fitting model to feature number 314, F327
## 2024-05-01 19:23:47.398172 INFO::Fitting model to feature number 315, F328
## 2024-05-01 19:23:47.40632 INFO::Fitting model to feature number 316, F329
## 2024-05-01 19:23:47.412491 INFO::Fitting model to feature number 317, F330
## 2024-05-01 19:23:47.418158 INFO::Fitting model to feature number 318, F331
## 2024-05-01 19:23:47.423416 INFO::Fitting model to feature number 319, F332
## 2024-05-01 19:23:47.428502 INFO::Fitting model to feature number 320, F333
## 2024-05-01 19:23:47.433652 INFO::Fitting model to feature number 321, F334
## 2024-05-01 19:23:47.441338 INFO::Fitting model to feature number 322, F335
## 2024-05-01 19:23:47.447708 INFO::Fitting model to feature number 323, F336
## 2024-05-01 19:23:47.453239 INFO::Fitting model to feature number 324, F337
## 2024-05-01 19:23:47.458635 INFO::Fitting model to feature number 325, F338
## 2024-05-01 19:23:47.463734 INFO::Fitting model to feature number 326, F339
## 2024-05-01 19:23:47.468587 INFO::Fitting model to feature number 327, F340
## 2024-05-01 19:23:47.473331 INFO::Fitting model to feature number 328, F342
## 2024-05-01 19:23:47.478251 INFO::Fitting model to feature number 329, F343
## 2024-05-01 19:23:47.483348 INFO::Fitting model to feature number 330, F344
## 2024-05-01 19:23:47.489463 INFO::Fitting model to feature number 331, F345
## 2024-05-01 19:23:47.494151 INFO::Fitting model to feature number 332, F346
## 2024-05-01 19:23:47.500203 INFO::Fitting model to feature number 333, F347
## 2024-05-01 19:23:47.507369 INFO::Fitting model to feature number 334, F348
## 2024-05-01 19:23:47.515261 INFO::Fitting model to feature number 335, F350
## 2024-05-01 19:23:47.52318 INFO::Fitting model to feature number 336, F351
## 2024-05-01 19:23:47.531307 INFO::Fitting model to feature number 337, F352
## 2024-05-01 19:23:47.539003 INFO::Fitting model to feature number 338, F353
## 2024-05-01 19:23:47.546867 INFO::Fitting model to feature number 339, F355
## 2024-05-01 19:23:47.554697 INFO::Fitting model to feature number 340, F356
## 2024-05-01 19:23:47.562022 INFO::Fitting model to feature number 341, F357
## 2024-05-01 19:23:47.567095 INFO::Fitting model to feature number 342, F358
## 2024-05-01 19:23:47.572665 INFO::Fitting model to feature number 343, F359
## 2024-05-01 19:23:47.578528 INFO::Fitting model to feature number 344, F360
## 2024-05-01 19:23:47.583176 INFO::Fitting model to feature number 345, F361
## 2024-05-01 19:23:47.588974 INFO::Fitting model to feature number 346, F362
## 2024-05-01 19:23:47.594626 INFO::Fitting model to feature number 347, F363
## 2024-05-01 19:23:47.600079 INFO::Fitting model to feature number 348, F364
## 2024-05-01 19:23:47.607341 INFO::Fitting model to feature number 349, F365
## 2024-05-01 19:23:47.613239 INFO::Fitting model to feature number 350, F366
## 2024-05-01 19:23:47.618357 INFO::Fitting model to feature number 351, F367
## 2024-05-01 19:23:47.62427 INFO::Fitting model to feature number 352, F368
## 2024-05-01 19:23:47.631227 INFO::Fitting model to feature number 353, F369
## 2024-05-01 19:23:47.639083 INFO::Fitting model to feature number 354, F370
## 2024-05-01 19:23:47.646847 INFO::Fitting model to feature number 355, F371
## 2024-05-01 19:23:47.654411 INFO::Fitting model to feature number 356, F372
## 2024-05-01 19:23:47.662032 INFO::Fitting model to feature number 357, F373
## 2024-05-01 19:23:47.669937 INFO::Fitting model to feature number 358, F374
## 2024-05-01 19:23:47.677758 INFO::Fitting model to feature number 359, F375
## 2024-05-01 19:23:47.686477 INFO::Fitting model to feature number 360, F376
## 2024-05-01 19:23:47.694182 INFO::Fitting model to feature number 361, F377
## 2024-05-01 19:23:47.701666 INFO::Fitting model to feature number 362, F378
## 2024-05-01 19:23:47.709203 INFO::Fitting model to feature number 363, F379
## 2024-05-01 19:23:47.7167 INFO::Fitting model to feature number 364, F380
## 2024-05-01 19:23:47.724359 INFO::Fitting model to feature number 365, F381
## 2024-05-01 19:23:47.73202 INFO::Fitting model to feature number 366, F382
## 2024-05-01 19:23:47.739605 INFO::Fitting model to feature number 367, F383
## 2024-05-01 19:23:47.747513 INFO::Fitting model to feature number 368, F384
## 2024-05-01 19:23:47.755325 INFO::Fitting model to feature number 369, F386
## 2024-05-01 19:23:47.76297 INFO::Fitting model to feature number 370, F387
## 2024-05-01 19:23:47.770862 INFO::Fitting model to feature number 371, F388
## 2024-05-01 19:23:47.778542 INFO::Fitting model to feature number 372, F389
## 2024-05-01 19:23:47.786114 INFO::Fitting model to feature number 373, F390
## 2024-05-01 19:23:47.79351 INFO::Fitting model to feature number 374, F391
## 2024-05-01 19:23:47.800934 INFO::Fitting model to feature number 375, F392
## 2024-05-01 19:23:47.808297 INFO::Fitting model to feature number 376, F393
## 2024-05-01 19:23:47.815934 INFO::Fitting model to feature number 377, F394
## 2024-05-01 19:23:47.8235 INFO::Fitting model to feature number 378, F395
## 2024-05-01 19:23:47.831142 INFO::Fitting model to feature number 379, F396
## 2024-05-01 19:23:47.838631 INFO::Fitting model to feature number 380, F397
## 2024-05-01 19:23:47.846342 INFO::Fitting model to feature number 381, F398
## 2024-05-01 19:23:47.853862 INFO::Fitting model to feature number 382, F399
## 2024-05-01 19:23:47.86153 INFO::Fitting model to feature number 383, F400
## 2024-05-01 19:23:47.868984 INFO::Fitting model to feature number 384, F401
## 2024-05-01 19:23:47.875978 INFO::Fitting model to feature number 385, F402
## 2024-05-01 19:23:47.880705 INFO::Fitting model to feature number 386, F403
## 2024-05-01 19:23:47.88542 INFO::Fitting model to feature number 387, F404
## 2024-05-01 19:23:47.890073 INFO::Fitting model to feature number 388, F406
## 2024-05-01 19:23:47.894717 INFO::Fitting model to feature number 389, F407
## 2024-05-01 19:23:47.899309 INFO::Fitting model to feature number 390, F408
## 2024-05-01 19:23:47.904186 INFO::Fitting model to feature number 391, F409
## 2024-05-01 19:23:47.911364 INFO::Fitting model to feature number 392, F410
## 2024-05-01 19:23:47.919171 INFO::Fitting model to feature number 393, F411
## 2024-05-01 19:23:47.926817 INFO::Fitting model to feature number 394, F412
## 2024-05-01 19:23:47.934436 INFO::Fitting model to feature number 395, F413
## 2024-05-01 19:23:47.942045 INFO::Fitting model to feature number 396, F414
## 2024-05-01 19:23:47.9497 INFO::Fitting model to feature number 397, F415
## 2024-05-01 19:23:47.9573 INFO::Fitting model to feature number 398, F416
## 2024-05-01 19:23:47.964854 INFO::Fitting model to feature number 399, F417
## 2024-05-01 19:23:47.973148 INFO::Fitting model to feature number 400, F418
## 2024-05-01 19:23:47.980905 INFO::Fitting model to feature number 401, F419
## 2024-05-01 19:23:47.988647 INFO::Fitting model to feature number 402, F420
## 2024-05-01 19:23:47.996233 INFO::Fitting model to feature number 403, F421
## 2024-05-01 19:23:48.004412 INFO::Fitting model to feature number 404, F422
## 2024-05-01 19:23:48.012633 INFO::Fitting model to feature number 405, F423
## 2024-05-01 19:23:48.021289 INFO::Fitting model to feature number 406, F425
## 2024-05-01 19:23:48.029793 INFO::Fitting model to feature number 407, F426
## 2024-05-01 19:23:48.042281 INFO::Fitting model to feature number 408, F428
## 2024-05-01 19:23:48.049419 INFO::Fitting model to feature number 409, F429
## 2024-05-01 19:23:48.054711 INFO::Fitting model to feature number 410, F430
## 2024-05-01 19:23:48.059895 INFO::Fitting model to feature number 411, F431
## 2024-05-01 19:23:48.065094 INFO::Fitting model to feature number 412, F432
## 2024-05-01 19:23:48.070129 INFO::Fitting model to feature number 413, F433
## 2024-05-01 19:23:48.076492 INFO::Fitting model to feature number 414, F434
## 2024-05-01 19:23:48.084798 INFO::Fitting model to feature number 415, F435
## 2024-05-01 19:23:48.093201 INFO::Fitting model to feature number 416, F436
## 2024-05-01 19:23:48.101362 INFO::Fitting model to feature number 417, F437
## 2024-05-01 19:23:48.109108 INFO::Fitting model to feature number 418, F438
## 2024-05-01 19:23:48.11681 INFO::Fitting model to feature number 419, F439
## 2024-05-01 19:23:48.124712 INFO::Fitting model to feature number 420, F440
## 2024-05-01 19:23:48.132812 INFO::Fitting model to feature number 421, F441
## 2024-05-01 19:23:48.140564 INFO::Fitting model to feature number 422, F442
## 2024-05-01 19:23:48.148155 INFO::Fitting model to feature number 423, F443
## 2024-05-01 19:23:48.155712 INFO::Fitting model to feature number 424, F444
## 2024-05-01 19:23:48.163116 INFO::Fitting model to feature number 425, F445
## 2024-05-01 19:23:48.170548 INFO::Fitting model to feature number 426, F446
## 2024-05-01 19:23:48.17822 INFO::Fitting model to feature number 427, F447
## 2024-05-01 19:23:48.185654 INFO::Fitting model to feature number 428, F448
## 2024-05-01 19:23:48.191398 INFO::Fitting model to feature number 429, F449
## 2024-05-01 19:23:48.196269 INFO::Fitting model to feature number 430, F450
## 2024-05-01 19:23:48.201091 INFO::Fitting model to feature number 431, F451
## 2024-05-01 19:23:48.206245 INFO::Fitting model to feature number 432, F452
## 2024-05-01 19:23:48.211085 INFO::Fitting model to feature number 433, F454
## 2024-05-01 19:23:48.216162 INFO::Fitting model to feature number 434, F455
## 2024-05-01 19:23:48.221132 INFO::Fitting model to feature number 435, F456
## 2024-05-01 19:23:48.225933 INFO::Fitting model to feature number 436, F457
## 2024-05-01 19:23:48.231169 INFO::Fitting model to feature number 437, F458
## 2024-05-01 19:23:48.235937 INFO::Fitting model to feature number 438, F459
## 2024-05-01 19:23:48.240658 INFO::Fitting model to feature number 439, F461
## 2024-05-01 19:23:48.246721 INFO::Fitting model to feature number 440, F462
## 2024-05-01 19:23:48.251955 INFO::Fitting model to feature number 441, F463
## 2024-05-01 19:23:48.25896 INFO::Fitting model to feature number 442, F464
## 2024-05-01 19:23:48.264817 INFO::Fitting model to feature number 443, F465
## 2024-05-01 19:23:48.272291 INFO::Fitting model to feature number 444, F466
## 2024-05-01 19:23:48.27951 INFO::Fitting model to feature number 445, F467
## 2024-05-01 19:23:48.28687 INFO::Fitting model to feature number 446, F468
## 2024-05-01 19:23:48.29405 INFO::Fitting model to feature number 447, F469
## 2024-05-01 19:23:48.302071 INFO::Fitting model to feature number 448, F470
## 2024-05-01 19:23:48.3105 INFO::Fitting model to feature number 449, F471
## 2024-05-01 19:23:48.31823 INFO::Fitting model to feature number 450, F474
## 2024-05-01 19:23:48.32659 INFO::Fitting model to feature number 451, F475
## 2024-05-01 19:23:48.334862 INFO::Fitting model to feature number 452, F476
## 2024-05-01 19:23:48.343165 INFO::Fitting model to feature number 453, F477
## 2024-05-01 19:23:48.349947 INFO::Fitting model to feature number 454, F478
## 2024-05-01 19:23:48.354961 INFO::Fitting model to feature number 455, F479
## 2024-05-01 19:23:48.361102 INFO::Fitting model to feature number 456, F480
## 2024-05-01 19:23:48.367636 INFO::Fitting model to feature number 457, F481
## 2024-05-01 19:23:48.373325 INFO::Fitting model to feature number 458, F482
## 2024-05-01 19:23:48.379949 INFO::Fitting model to feature number 459, F483
## 2024-05-01 19:23:48.388709 INFO::Fitting model to feature number 460, F484
## 2024-05-01 19:23:48.396872 INFO::Fitting model to feature number 461, F485
## 2024-05-01 19:23:48.404951 INFO::Fitting model to feature number 462, F486
## 2024-05-01 19:23:48.413232 INFO::Fitting model to feature number 463, F487
## 2024-05-01 19:23:48.421503 INFO::Fitting model to feature number 464, F488
## 2024-05-01 19:23:48.429963 INFO::Fitting model to feature number 465, F489
## 2024-05-01 19:23:48.438304 INFO::Fitting model to feature number 466, F490
## 2024-05-01 19:23:48.446702 INFO::Fitting model to feature number 467, F491
## 2024-05-01 19:23:48.455052 INFO::Fitting model to feature number 468, F492
## 2024-05-01 19:23:48.463259 INFO::Fitting model to feature number 469, F493
## 2024-05-01 19:23:48.471262 INFO::Fitting model to feature number 470, F494
## 2024-05-01 19:23:48.479599 INFO::Fitting model to feature number 471, F495
## 2024-05-01 19:23:48.487775 INFO::Fitting model to feature number 472, F496
## 2024-05-01 19:23:48.495657 INFO::Fitting model to feature number 473, F497
## 2024-05-01 19:23:48.503702 INFO::Fitting model to feature number 474, F498
## 2024-05-01 19:23:48.509261 INFO::Fitting model to feature number 475, F499
## 2024-05-01 19:23:48.514498 INFO::Fitting model to feature number 476, F500
## 2024-05-01 19:23:48.521332 INFO::Fitting model to feature number 477, F501
## 2024-05-01 19:23:48.526416 INFO::Fitting model to feature number 478, F502
## 2024-05-01 19:23:48.531366 INFO::Fitting model to feature number 479, F503
## 2024-05-01 19:23:48.536439 INFO::Fitting model to feature number 480, F504
## 2024-05-01 19:23:48.541571 INFO::Fitting model to feature number 481, F505
## 2024-05-01 19:23:48.546839 INFO::Fitting model to feature number 482, F506
## 2024-05-01 19:23:48.551957 INFO::Fitting model to feature number 483, F507
## 2024-05-01 19:23:48.556934 INFO::Fitting model to feature number 484, F508
## 2024-05-01 19:23:48.562 INFO::Fitting model to feature number 485, F509
## 2024-05-01 19:23:48.567036 INFO::Fitting model to feature number 486, F510
## 2024-05-01 19:23:48.572008 INFO::Fitting model to feature number 487, F511
## 2024-05-01 19:23:48.577084 INFO::Fitting model to feature number 488, F512
## 2024-05-01 19:23:48.582235 INFO::Fitting model to feature number 489, F513
## 2024-05-01 19:23:48.587338 INFO::Fitting model to feature number 490, F514
## 2024-05-01 19:23:48.592637 INFO::Fitting model to feature number 491, F515
## 2024-05-01 19:23:48.597727 INFO::Fitting model to feature number 492, F516
## 2024-05-01 19:23:48.602934 INFO::Fitting model to feature number 493, F517
## 2024-05-01 19:23:48.610897 INFO::Fitting model to feature number 494, F518
## 2024-05-01 19:23:48.618699 INFO::Fitting model to feature number 495, F519
## 2024-05-01 19:23:48.626635 INFO::Fitting model to feature number 496, F520
## 2024-05-01 19:23:48.634601 INFO::Fitting model to feature number 497, F521
## 2024-05-01 19:23:48.642635 INFO::Fitting model to feature number 498, F522
## 2024-05-01 19:23:48.650569 INFO::Fitting model to feature number 499, F523
## 2024-05-01 19:23:48.65861 INFO::Fitting model to feature number 500, F524
## 2024-05-01 19:23:48.666485 INFO::Fitting model to feature number 501, F525
## 2024-05-01 19:23:48.674412 INFO::Fitting model to feature number 502, F526
## 2024-05-01 19:23:48.680936 INFO::Fitting model to feature number 503, F527
## 2024-05-01 19:23:48.686642 INFO::Fitting model to feature number 504, F528
## 2024-05-01 19:23:48.691882 INFO::Fitting model to feature number 505, F529
## 2024-05-01 19:23:48.69694 INFO::Fitting model to feature number 506, F530
## 2024-05-01 19:23:48.701956 INFO::Fitting model to feature number 507, F531
## 2024-05-01 19:23:48.707041 INFO::Fitting model to feature number 508, F532
## 2024-05-01 19:23:48.712116 INFO::Fitting model to feature number 509, F533
## 2024-05-01 19:23:48.717968 INFO::Fitting model to feature number 510, F534
## 2024-05-01 19:23:48.722927 INFO::Fitting model to feature number 511, F535
## 2024-05-01 19:23:48.727865 INFO::Fitting model to feature number 512, F536
## 2024-05-01 19:23:48.733041 INFO::Fitting model to feature number 513, F537
## 2024-05-01 19:23:48.738242 INFO::Fitting model to feature number 514, F539
## 2024-05-01 19:23:48.7432 INFO::Fitting model to feature number 515, F540
## 2024-05-01 19:23:48.748478 INFO::Fitting model to feature number 516, F541
## 2024-05-01 19:23:48.75408 INFO::Fitting model to feature number 517, F543
## 2024-05-01 19:23:48.759234 INFO::Fitting model to feature number 518, F544
## 2024-05-01 19:23:48.764155 INFO::Fitting model to feature number 519, F545
## 2024-05-01 19:23:48.769084 INFO::Fitting model to feature number 520, F546
## 2024-05-01 19:23:48.774472 INFO::Fitting model to feature number 521, F547
## 2024-05-01 19:23:48.779697 INFO::Fitting model to feature number 522, F548
## 2024-05-01 19:23:48.784614 INFO::Fitting model to feature number 523, F549
## 2024-05-01 19:23:48.789719 INFO::Fitting model to feature number 524, F550
## 2024-05-01 19:23:48.794725 INFO::Fitting model to feature number 525, F551
## 2024-05-01 19:23:48.799817 INFO::Fitting model to feature number 526, F552
## 2024-05-01 19:23:48.804868 INFO::Fitting model to feature number 527, F553
## 2024-05-01 19:23:48.810224 INFO::Fitting model to feature number 528, F554
## 2024-05-01 19:23:48.817157 INFO::Fitting model to feature number 529, F555
## 2024-05-01 19:23:48.824978 INFO::Fitting model to feature number 530, F556
## 2024-05-01 19:23:48.83251 INFO::Fitting model to feature number 531, F557
## 2024-05-01 19:23:48.840023 INFO::Fitting model to feature number 532, F558
## 2024-05-01 19:23:48.847644 INFO::Fitting model to feature number 533, F559
## 2024-05-01 19:23:48.855485 INFO::Fitting model to feature number 534, F560
## 2024-05-01 19:23:48.863411 INFO::Fitting model to feature number 535, F561
## 2024-05-01 19:23:48.871209 INFO::Fitting model to feature number 536, F562
## 2024-05-01 19:23:48.87907 INFO::Fitting model to feature number 537, F563
## 2024-05-01 19:23:48.887062 INFO::Fitting model to feature number 538, F564
## 2024-05-01 19:23:48.895085 INFO::Fitting model to feature number 539, F566
## 2024-05-01 19:23:48.903027 INFO::Fitting model to feature number 540, F567
## 2024-05-01 19:23:48.911003 INFO::Fitting model to feature number 541, F568
## 2024-05-01 19:23:48.91892 INFO::Fitting model to feature number 542, F569
## 2024-05-01 19:23:48.926797 INFO::Fitting model to feature number 543, F570
## 2024-05-01 19:23:48.934642 INFO::Fitting model to feature number 544, F571
## 2024-05-01 19:23:48.942596 INFO::Fitting model to feature number 545, F572
## 2024-05-01 19:23:48.950447 INFO::Fitting model to feature number 546, F573
## 2024-05-01 19:23:48.958213 INFO::Fitting model to feature number 547, F574
## 2024-05-01 19:23:48.966007 INFO::Fitting model to feature number 548, F575
## 2024-05-01 19:23:48.974223 INFO::Fitting model to feature number 549, F576
## 2024-05-01 19:23:48.982124 INFO::Fitting model to feature number 550, F577
## 2024-05-01 19:23:48.990127 INFO::Fitting model to feature number 551, F578
## 2024-05-01 19:23:48.998241 INFO::Fitting model to feature number 552, F579
## 2024-05-01 19:23:49.00466 INFO::Fitting model to feature number 553, F580
## 2024-05-01 19:23:49.009845 INFO::Fitting model to feature number 554, F581
## 2024-05-01 19:23:49.014982 INFO::Fitting model to feature number 555, F582
## 2024-05-01 19:23:49.021509 INFO::Fitting model to feature number 556, F583
## 2024-05-01 19:23:49.026679 INFO::Fitting model to feature number 557, F584
## 2024-05-01 19:23:49.031737 INFO::Fitting model to feature number 558, F585
## 2024-05-01 19:23:49.036718 INFO::Fitting model to feature number 559, F586
## 2024-05-01 19:23:49.041621 INFO::Fitting model to feature number 560, F587
## 2024-05-01 19:23:49.04658 INFO::Fitting model to feature number 561, F588
## 2024-05-01 19:23:49.051528 INFO::Fitting model to feature number 562, F589
## 2024-05-01 19:23:49.056631 INFO::Fitting model to feature number 563, F590
## 2024-05-01 19:23:49.06156 INFO::Fitting model to feature number 564, F591
## 2024-05-01 19:23:49.066439 INFO::Fitting model to feature number 565, F592
## 2024-05-01 19:23:49.071484 INFO::Fitting model to feature number 566, F593
## 2024-05-01 19:23:49.076762 INFO::Fitting model to feature number 567, F594
## 2024-05-01 19:23:49.081955 INFO::Fitting model to feature number 568, F595
## 2024-05-01 19:23:49.087033 INFO::Fitting model to feature number 569, F596
## 2024-05-01 19:23:49.092118 INFO::Fitting model to feature number 570, F597
## 2024-05-01 19:23:49.097215 INFO::Fitting model to feature number 571, F598
## 2024-05-01 19:23:49.102256 INFO::Fitting model to feature number 572, F599
## 2024-05-01 19:23:49.107305 INFO::Fitting model to feature number 573, F600
## 2024-05-01 19:23:49.112429 INFO::Fitting model to feature number 574, F601
## 2024-05-01 19:23:49.117479 INFO::Fitting model to feature number 575, F602
## 2024-05-01 19:23:49.122593 INFO::Fitting model to feature number 576, F603
## 2024-05-01 19:23:49.127951 INFO::Fitting model to feature number 577, F605
## 2024-05-01 19:23:49.133044 INFO::Fitting model to feature number 578, F606
## 2024-05-01 19:23:49.138132 INFO::Fitting model to feature number 579, F607
## 2024-05-01 19:23:49.143483 INFO::Fitting model to feature number 580, F608
## 2024-05-01 19:23:49.150845 INFO::Fitting model to feature number 581, F609
## 2024-05-01 19:23:49.156748 INFO::Fitting model to feature number 582, F610
## 2024-05-01 19:23:49.161858 INFO::Fitting model to feature number 583, F611
## 2024-05-01 19:23:49.166916 INFO::Fitting model to feature number 584, F612
## 2024-05-01 19:23:49.172028 INFO::Fitting model to feature number 585, F613
## 2024-05-01 19:23:49.177176 INFO::Fitting model to feature number 586, F614
## 2024-05-01 19:23:49.182247 INFO::Fitting model to feature number 587, F615
## 2024-05-01 19:23:49.187392 INFO::Fitting model to feature number 588, F616
## 2024-05-01 19:23:49.192496 INFO::Fitting model to feature number 589, F617
## 2024-05-01 19:23:49.197471 INFO::Fitting model to feature number 590, F618
## 2024-05-01 19:23:49.202572 INFO::Fitting model to feature number 591, F619
## 2024-05-01 19:23:49.207742 INFO::Fitting model to feature number 592, F620
## 2024-05-01 19:23:49.212879 INFO::Fitting model to feature number 593, F621
## 2024-05-01 19:23:49.218091 INFO::Fitting model to feature number 594, F622
## 2024-05-01 19:23:49.223267 INFO::Fitting model to feature number 595, F623
## 2024-05-01 19:23:49.228302 INFO::Fitting model to feature number 596, F624
## 2024-05-01 19:23:49.233927 INFO::Fitting model to feature number 597, F625
## 2024-05-01 19:23:49.241012 INFO::Fitting model to feature number 598, F626
## 2024-05-01 19:23:49.248934 INFO::Fitting model to feature number 599, F627
## 2024-05-01 19:23:49.25525 INFO::Fitting model to feature number 600, F628
## 2024-05-01 19:23:49.285485 INFO::Fitting model to feature number 601, F629
## 2024-05-01 19:23:49.290961 INFO::Fitting model to feature number 602, F630
## 2024-05-01 19:23:49.296067 INFO::Fitting model to feature number 603, F631
## 2024-05-01 19:23:49.30091 INFO::Fitting model to feature number 604, F632
## 2024-05-01 19:23:49.305897 INFO::Fitting model to feature number 605, F633
## 2024-05-01 19:23:49.310873 INFO::Fitting model to feature number 606, F634
## 2024-05-01 19:23:49.316261 INFO::Fitting model to feature number 607, F635
## 2024-05-01 19:23:49.32206 INFO::Fitting model to feature number 608, F636
## 2024-05-01 19:23:49.327494 INFO::Fitting model to feature number 609, F637
## 2024-05-01 19:23:49.333075 INFO::Fitting model to feature number 610, F638
## 2024-05-01 19:23:49.337879 INFO::Fitting model to feature number 611, F639
## 2024-05-01 19:23:49.343671 INFO::Fitting model to feature number 612, F640
## 2024-05-01 19:23:49.349801 INFO::Fitting model to feature number 613, F641
## 2024-05-01 19:23:49.357099 INFO::Fitting model to feature number 614, F642
## 2024-05-01 19:23:49.363956 INFO::Fitting model to feature number 615, F643
## 2024-05-01 19:23:49.369899 INFO::Fitting model to feature number 616, F644
## 2024-05-01 19:23:49.374792 INFO::Fitting model to feature number 617, F645
## 2024-05-01 19:23:49.380608 INFO::Fitting model to feature number 618, F646
## 2024-05-01 19:23:49.388309 INFO::Fitting model to feature number 619, F647
## 2024-05-01 19:23:49.394639 INFO::Fitting model to feature number 620, F648
## 2024-05-01 19:23:49.400767 INFO::Fitting model to feature number 621, F649
## 2024-05-01 19:23:49.405652 INFO::Fitting model to feature number 622, F650
## 2024-05-01 19:23:49.412044 INFO::Fitting model to feature number 623, F651
## 2024-05-01 19:23:49.418969 INFO::Fitting model to feature number 624, F652
## 2024-05-01 19:23:49.426281 INFO::Fitting model to feature number 625, F653
## 2024-05-01 19:23:49.433708 INFO::Fitting model to feature number 626, F654
## 2024-05-01 19:23:49.440412 INFO::Fitting model to feature number 627, F655
## 2024-05-01 19:23:49.447975 INFO::Fitting model to feature number 628, F656
## 2024-05-01 19:23:49.455955 INFO::Fitting model to feature number 629, F657
## 2024-05-01 19:23:49.461007 INFO::Fitting model to feature number 630, F658
## 2024-05-01 19:23:49.467074 INFO::Fitting model to feature number 631, F659
## 2024-05-01 19:23:49.47211 INFO::Fitting model to feature number 632, F660
## 2024-05-01 19:23:49.476958 INFO::Fitting model to feature number 633, F661
## 2024-05-01 19:23:49.482326 INFO::Fitting model to feature number 634, F662
## 2024-05-01 19:23:49.487924 INFO::Fitting model to feature number 635, F663
## 2024-05-01 19:23:49.495198 INFO::Fitting model to feature number 636, F664
## 2024-05-01 19:23:49.502955 INFO::Fitting model to feature number 637, F665
## 2024-05-01 19:23:49.510995 INFO::Fitting model to feature number 638, F666
## 2024-05-01 19:23:49.519377 INFO::Fitting model to feature number 639, F667
## 2024-05-01 19:23:49.527555 INFO::Fitting model to feature number 640, F668
## 2024-05-01 19:23:49.535398 INFO::Fitting model to feature number 641, F669
## 2024-05-01 19:23:49.543631 INFO::Fitting model to feature number 642, F670
## 2024-05-01 19:23:49.552006 INFO::Fitting model to feature number 643, F671
## 2024-05-01 19:23:49.560244 INFO::Fitting model to feature number 644, F672
## 2024-05-01 19:23:49.568427 INFO::Fitting model to feature number 645, F673
## 2024-05-01 19:23:49.576886 INFO::Fitting model to feature number 646, F674
## 2024-05-01 19:23:49.585017 INFO::Fitting model to feature number 647, F675
## 2024-05-01 19:23:49.593075 INFO::Fitting model to feature number 648, F676
## 2024-05-01 19:23:49.601257 INFO::Fitting model to feature number 649, F677
## 2024-05-01 19:23:49.609275 INFO::Fitting model to feature number 650, F678
## 2024-05-01 19:23:49.617753 INFO::Fitting model to feature number 651, F679
## 2024-05-01 19:23:49.622787 INFO::Fitting model to feature number 652, F680
## 2024-05-01 19:23:49.627825 INFO::Fitting model to feature number 653, F681
## 2024-05-01 19:23:49.633586 INFO::Fitting model to feature number 654, F682
## 2024-05-01 19:23:49.639364 INFO::Fitting model to feature number 655, F683
## 2024-05-01 19:23:49.64765 INFO::Fitting model to feature number 656, F684
## 2024-05-01 19:23:49.655969 INFO::Fitting model to feature number 657, F685
## 2024-05-01 19:23:49.66153 INFO::Fitting model to feature number 658, F686
## 2024-05-01 19:23:49.667123 INFO::Fitting model to feature number 659, F687
## 2024-05-01 19:23:49.672051 INFO::Fitting model to feature number 660, F688
## 2024-05-01 19:23:49.676923 INFO::Fitting model to feature number 661, F689
## 2024-05-01 19:23:49.681754 INFO::Fitting model to feature number 662, F690
## 2024-05-01 19:23:49.687465 INFO::Fitting model to feature number 663, F691
## 2024-05-01 19:23:49.692863 INFO::Fitting model to feature number 664, F692
## 2024-05-01 19:23:49.698103 INFO::Fitting model to feature number 665, F693
## 2024-05-01 19:23:49.703718 INFO::Fitting model to feature number 666, F694
## 2024-05-01 19:23:49.709309 INFO::Fitting model to feature number 667, F695
## 2024-05-01 19:23:49.714605 INFO::Fitting model to feature number 668, F696
## 2024-05-01 19:23:49.719463 INFO::Fitting model to feature number 669, F697
## 2024-05-01 19:23:49.724792 INFO::Fitting model to feature number 670, F698
## 2024-05-01 19:23:49.729734 INFO::Fitting model to feature number 671, F699
## 2024-05-01 19:23:49.734618 INFO::Fitting model to feature number 672, F700
## 2024-05-01 19:23:49.739436 INFO::Fitting model to feature number 673, F701
## 2024-05-01 19:23:49.744269 INFO::Fitting model to feature number 674, F702
## 2024-05-01 19:23:49.749722 INFO::Fitting model to feature number 675, F704
## 2024-05-01 19:23:49.755805 INFO::Fitting model to feature number 676, F705
## 2024-05-01 19:23:49.761406 INFO::Fitting model to feature number 677, F706
## 2024-05-01 19:23:49.766452 INFO::Fitting model to feature number 678, F707
## 2024-05-01 19:23:49.771814 INFO::Fitting model to feature number 679, F708
## 2024-05-01 19:23:49.77686 INFO::Fitting model to feature number 680, F709
## 2024-05-01 19:23:49.781805 INFO::Fitting model to feature number 681, F710
## 2024-05-01 19:23:49.78959 INFO::Fitting model to feature number 682, F711
## 2024-05-01 19:23:49.79725 INFO::Fitting model to feature number 683, F712
## 2024-05-01 19:23:49.802768 INFO::Fitting model to feature number 684, F713
## 2024-05-01 19:23:49.807941 INFO::Fitting model to feature number 685, F714
## 2024-05-01 19:23:49.81512 INFO::Fitting model to feature number 686, F715
## 2024-05-01 19:23:49.823596 INFO::Fitting model to feature number 687, F716
## 2024-05-01 19:23:49.830171 INFO::Fitting model to feature number 688, F717
## 2024-05-01 19:23:49.836318 INFO::Fitting model to feature number 689, F718
## 2024-05-01 19:23:49.841441 INFO::Fitting model to feature number 690, F719
## 2024-05-01 19:23:49.846523 INFO::Fitting model to feature number 691, F720
## 2024-05-01 19:23:49.854051 INFO::Fitting model to feature number 692, F721
## 2024-05-01 19:23:49.862125 INFO::Fitting model to feature number 693, F722
## 2024-05-01 19:23:49.86858 INFO::Fitting model to feature number 694, F723
## 2024-05-01 19:23:49.873832 INFO::Fitting model to feature number 695, F724
## 2024-05-01 19:23:49.880104 INFO::Fitting model to feature number 696, F725
## 2024-05-01 19:23:49.888017 INFO::Fitting model to feature number 697, F726
## 2024-05-01 19:23:49.894995 INFO::Fitting model to feature number 698, F727
## 2024-05-01 19:23:49.90198 INFO::Fitting model to feature number 699, F728
## 2024-05-01 19:23:49.909818 INFO::Fitting model to feature number 700, F729
## 2024-05-01 19:23:49.915028 INFO::Fitting model to feature number 701, F730
## 2024-05-01 19:23:49.919887 INFO::Fitting model to feature number 702, F731
## 2024-05-01 19:23:49.924784 INFO::Fitting model to feature number 703, F732
## 2024-05-01 19:23:49.929907 INFO::Fitting model to feature number 704, F733
## 2024-05-01 19:23:49.934785 INFO::Fitting model to feature number 705, F734
## 2024-05-01 19:23:49.940462 INFO::Fitting model to feature number 706, F735
## 2024-05-01 19:23:49.949147 INFO::Fitting model to feature number 707, F736
## 2024-05-01 19:23:49.956339 INFO::Fitting model to feature number 708, F737
## 2024-05-01 19:23:49.961421 INFO::Fitting model to feature number 709, F739
## 2024-05-01 19:23:49.968247 INFO::Fitting model to feature number 710, F740
## 2024-05-01 19:23:49.975269 INFO::Fitting model to feature number 711, F741
## 2024-05-01 19:23:49.980162 INFO::Fitting model to feature number 712, F742
## 2024-05-01 19:23:49.987829 INFO::Fitting model to feature number 713, F743
## 2024-05-01 19:23:49.993319 INFO::Fitting model to feature number 714, F744
## 2024-05-01 19:23:49.998711 INFO::Fitting model to feature number 715, F745
## 2024-05-01 19:23:50.004995 INFO::Fitting model to feature number 716, F746
## 2024-05-01 19:23:50.012719 INFO::Fitting model to feature number 717, F747
## 2024-05-01 19:23:50.020595 INFO::Fitting model to feature number 718, F748
## 2024-05-01 19:23:50.028174 INFO::Fitting model to feature number 719, F749
## 2024-05-01 19:23:50.03576 INFO::Fitting model to feature number 720, F750
## 2024-05-01 19:23:50.042226 INFO::Fitting model to feature number 721, F751
## 2024-05-01 19:23:50.04776 INFO::Fitting model to feature number 722, F752
## 2024-05-01 19:23:50.053239 INFO::Fitting model to feature number 723, F753
## 2024-05-01 19:23:50.05827 INFO::Fitting model to feature number 724, F754
## 2024-05-01 19:23:50.063373 INFO::Fitting model to feature number 725, F755
## 2024-05-01 19:23:50.068327 INFO::Fitting model to feature number 726, F756
## 2024-05-01 19:23:50.073554 INFO::Fitting model to feature number 727, F757
## 2024-05-01 19:23:50.07861 INFO::Fitting model to feature number 728, F758
## 2024-05-01 19:23:50.083641 INFO::Fitting model to feature number 729, F759
## 2024-05-01 19:23:50.08869 INFO::Fitting model to feature number 730, F760
## 2024-05-01 19:23:50.093643 INFO::Fitting model to feature number 731, F761
## 2024-05-01 19:23:50.098722 INFO::Fitting model to feature number 732, F762
## 2024-05-01 19:23:50.103849 INFO::Fitting model to feature number 733, F763
## 2024-05-01 19:23:50.108831 INFO::Fitting model to feature number 734, F764
## 2024-05-01 19:23:50.113806 INFO::Fitting model to feature number 735, F765
## 2024-05-01 19:23:50.118654 INFO::Fitting model to feature number 736, F766
## 2024-05-01 19:23:50.124075 INFO::Fitting model to feature number 737, F767
## 2024-05-01 19:23:50.129024 INFO::Fitting model to feature number 738, F768
## 2024-05-01 19:23:50.134454 INFO::Fitting model to feature number 739, F769
## 2024-05-01 19:23:50.13953 INFO::Fitting model to feature number 740, F770
## 2024-05-01 19:23:50.144502 INFO::Fitting model to feature number 741, F771
## 2024-05-01 19:23:50.149385 INFO::Fitting model to feature number 742, F772
## 2024-05-01 19:23:50.154229 INFO::Fitting model to feature number 743, F773
## 2024-05-01 19:23:50.159097 INFO::Fitting model to feature number 744, F774
## 2024-05-01 19:23:50.163865 INFO::Fitting model to feature number 745, F775
## 2024-05-01 19:23:50.168682 INFO::Fitting model to feature number 746, F776
## 2024-05-01 19:23:50.173458 INFO::Fitting model to feature number 747, F777
## 2024-05-01 19:23:50.178183 INFO::Fitting model to feature number 748, F778
## 2024-05-01 19:23:50.182993 INFO::Fitting model to feature number 749, F779
## 2024-05-01 19:23:50.187804 INFO::Fitting model to feature number 750, F780
## 2024-05-01 19:23:50.193051 INFO::Fitting model to feature number 751, F781
## 2024-05-01 19:23:50.200055 INFO::Fitting model to feature number 752, F782
## 2024-05-01 19:23:50.207692 INFO::Fitting model to feature number 753, F783
## 2024-05-01 19:23:50.212846 INFO::Fitting model to feature number 754, F784
## 2024-05-01 19:23:50.217914 INFO::Fitting model to feature number 755, F785
## 2024-05-01 19:23:50.222755 INFO::Fitting model to feature number 756, F786
## 2024-05-01 19:23:50.227628 INFO::Fitting model to feature number 757, F787
## 2024-05-01 19:23:50.23254 INFO::Fitting model to feature number 758, F788
## 2024-05-01 19:23:50.237742 INFO::Fitting model to feature number 759, F789
## 2024-05-01 19:23:50.242867 INFO::Fitting model to feature number 760, F790
## 2024-05-01 19:23:50.247756 INFO::Fitting model to feature number 761, F791
## 2024-05-01 19:23:50.252718 INFO::Fitting model to feature number 762, F792
## 2024-05-01 19:23:50.258934 INFO::Fitting model to feature number 763, F793
## 2024-05-01 19:23:50.266978 INFO::Fitting model to feature number 764, F794
## 2024-05-01 19:23:50.275356 INFO::Fitting model to feature number 765, F795
## 2024-05-01 19:23:50.282824 INFO::Fitting model to feature number 766, F796
## 2024-05-01 19:23:50.290395 INFO::Fitting model to feature number 767, F797
## 2024-05-01 19:23:50.298002 INFO::Fitting model to feature number 768, F798
## 2024-05-01 19:23:50.305537 INFO::Fitting model to feature number 769, F799
## 2024-05-01 19:23:50.313352 INFO::Fitting model to feature number 770, F800
## 2024-05-01 19:23:50.321155 INFO::Fitting model to feature number 771, F801
## 2024-05-01 19:23:50.329201 INFO::Fitting model to feature number 772, F802
## 2024-05-01 19:23:50.336831 INFO::Fitting model to feature number 773, F803
## 2024-05-01 19:23:50.34327 INFO::Fitting model to feature number 774, F804
## 2024-05-01 19:23:50.350437 INFO::Fitting model to feature number 775, F805
## 2024-05-01 19:23:50.3589 INFO::Fitting model to feature number 776, F806
## 2024-05-01 19:23:50.36622 INFO::Fitting model to feature number 777, F808
## 2024-05-01 19:23:50.372853 INFO::Fitting model to feature number 778, F809
## 2024-05-01 19:23:50.379257 INFO::Fitting model to feature number 779, F810
## 2024-05-01 19:23:50.386999 INFO::Fitting model to feature number 780, F811
## 2024-05-01 19:23:50.395193 INFO::Fitting model to feature number 781, F812
## 2024-05-01 19:23:50.403343 INFO::Fitting model to feature number 782, F813
## 2024-05-01 19:23:50.411666 INFO::Fitting model to feature number 783, F814
## 2024-05-01 19:23:50.418322 INFO::Fitting model to feature number 784, F815
## 2024-05-01 19:23:50.425708 INFO::Fitting model to feature number 785, F816
## 2024-05-01 19:23:50.43438 INFO::Fitting model to feature number 786, F817
## 2024-05-01 19:23:50.441291 INFO::Fitting model to feature number 787, F818
## 2024-05-01 19:23:50.446841 INFO::Fitting model to feature number 788, F819
## 2024-05-01 19:23:50.452918 INFO::Fitting model to feature number 789, F820
## 2024-05-01 19:23:50.45813 INFO::Fitting model to feature number 790, F821
## 2024-05-01 19:23:50.463175 INFO::Fitting model to feature number 791, F822
## 2024-05-01 19:23:50.469959 INFO::Fitting model to feature number 792, F823
## 2024-05-01 19:23:50.476027 INFO::Fitting model to feature number 793, F824
## 2024-05-01 19:23:50.481598 INFO::Fitting model to feature number 794, F825
## 2024-05-01 19:23:50.487703 INFO::Fitting model to feature number 795, F826
## 2024-05-01 19:23:50.495455 INFO::Fitting model to feature number 796, F827
## 2024-05-01 19:23:50.50377 INFO::Fitting model to feature number 797, F828
## 2024-05-01 19:23:50.511777 INFO::Fitting model to feature number 798, F829
## 2024-05-01 19:23:50.519745 INFO::Fitting model to feature number 799, F830
## 2024-05-01 19:23:50.525222 INFO::Fitting model to feature number 800, F831
## 2024-05-01 19:23:50.53031 INFO::Fitting model to feature number 801, F832
## 2024-05-01 19:23:50.536293 INFO::Fitting model to feature number 802, F833
## 2024-05-01 19:23:50.542097 INFO::Fitting model to feature number 803, F834
## 2024-05-01 19:23:50.548987 INFO::Fitting model to feature number 804, F835
## 2024-05-01 19:23:50.554317 INFO::Fitting model to feature number 805, F836
## 2024-05-01 19:23:50.559621 INFO::Fitting model to feature number 806, F837
## 2024-05-01 19:23:50.564881 INFO::Fitting model to feature number 807, F838
## 2024-05-01 19:23:50.570029 INFO::Fitting model to feature number 808, F839
## 2024-05-01 19:23:50.575246 INFO::Fitting model to feature number 809, F840
## 2024-05-01 19:23:50.580402 INFO::Fitting model to feature number 810, F841
## 2024-05-01 19:23:50.585466 INFO::Fitting model to feature number 811, F842
## 2024-05-01 19:23:50.590566 INFO::Fitting model to feature number 812, F843
## 2024-05-01 19:23:50.595803 INFO::Fitting model to feature number 813, F844
## 2024-05-01 19:23:50.600905 INFO::Fitting model to feature number 814, F845
## 2024-05-01 19:23:50.606664 INFO::Fitting model to feature number 815, F846
## 2024-05-01 19:23:50.613189 INFO::Fitting model to feature number 816, F847
## 2024-05-01 19:23:50.621374 INFO::Fitting model to feature number 817, F848
## 2024-05-01 19:23:50.62958 INFO::Fitting model to feature number 818, F849
## 2024-05-01 19:23:50.637702 INFO::Fitting model to feature number 819, F850
## 2024-05-01 19:23:50.645848 INFO::Fitting model to feature number 820, F851
## 2024-05-01 19:23:50.654057 INFO::Fitting model to feature number 821, F852
## 2024-05-01 19:23:50.662321 INFO::Fitting model to feature number 822, F853
## 2024-05-01 19:23:50.670052 INFO::Fitting model to feature number 823, F854
## 2024-05-01 19:23:50.676177 INFO::Fitting model to feature number 824, F855
## 2024-05-01 19:23:50.683987 INFO::Fitting model to feature number 825, F856
## 2024-05-01 19:23:50.689222 INFO::Fitting model to feature number 826, F857
## 2024-05-01 19:23:50.69436 INFO::Fitting model to feature number 827, F858
## 2024-05-01 19:23:50.699501 INFO::Fitting model to feature number 828, F859
## 2024-05-01 19:23:50.704565 INFO::Fitting model to feature number 829, F860
## 2024-05-01 19:23:50.709771 INFO::Fitting model to feature number 830, F861
## 2024-05-01 19:23:50.714895 INFO::Fitting model to feature number 831, F862
## 2024-05-01 19:23:50.720053 INFO::Fitting model to feature number 832, F863
## 2024-05-01 19:23:50.725251 INFO::Fitting model to feature number 833, F864
## 2024-05-01 19:23:50.730385 INFO::Fitting model to feature number 834, F865
## 2024-05-01 19:23:50.73541 INFO::Fitting model to feature number 835, F866
## 2024-05-01 19:23:50.740536 INFO::Fitting model to feature number 836, F867
## 2024-05-01 19:23:50.745604 INFO::Fitting model to feature number 837, F868
## 2024-05-01 19:23:50.750735 INFO::Fitting model to feature number 838, F869
## 2024-05-01 19:23:50.755784 INFO::Fitting model to feature number 839, F870
## 2024-05-01 19:23:50.760957 INFO::Fitting model to feature number 840, F871
## 2024-05-01 19:23:50.766108 INFO::Fitting model to feature number 841, F872
## 2024-05-01 19:23:50.771563 INFO::Fitting model to feature number 842, F873
## 2024-05-01 19:23:50.777293 INFO::Fitting model to feature number 843, F874
## 2024-05-01 19:23:50.782983 INFO::Fitting model to feature number 844, F875
## 2024-05-01 19:23:50.790124 INFO::Fitting model to feature number 845, F876
## 2024-05-01 19:23:50.798487 INFO::Fitting model to feature number 846, F877
## 2024-05-01 19:23:50.806601 INFO::Fitting model to feature number 847, F878
## 2024-05-01 19:23:50.814921 INFO::Fitting model to feature number 848, F879
## 2024-05-01 19:23:50.821283 INFO::Fitting model to feature number 849, F880
## 2024-05-01 19:23:50.829398 INFO::Fitting model to feature number 850, F881
## 2024-05-01 19:23:50.834581 INFO::Fitting model to feature number 851, F882
## 2024-05-01 19:23:50.840046 INFO::Fitting model to feature number 852, F883
## 2024-05-01 19:23:50.84569 INFO::Fitting model to feature number 853, F884
## 2024-05-01 19:23:50.852215 INFO::Fitting model to feature number 854, F885
## 2024-05-01 19:23:50.858775 INFO::Fitting model to feature number 855, F886
## 2024-05-01 19:23:50.866824 INFO::Fitting model to feature number 856, F887
## 2024-05-01 19:23:50.875169 INFO::Fitting model to feature number 857, F888
## 2024-05-01 19:23:50.883517 INFO::Fitting model to feature number 858, F889
## 2024-05-01 19:23:50.891548 INFO::Fitting model to feature number 859, F890
## 2024-05-01 19:23:50.899934 INFO::Fitting model to feature number 860, F891
## 2024-05-01 19:23:50.908061 INFO::Fitting model to feature number 861, F892
## 2024-05-01 19:23:50.916272 INFO::Fitting model to feature number 862, F893
## 2024-05-01 19:23:50.924498 INFO::Fitting model to feature number 863, F894
## 2024-05-01 19:23:50.932458 INFO::Fitting model to feature number 864, F895
## 2024-05-01 19:23:50.940163 INFO::Fitting model to feature number 865, F896
## 2024-05-01 19:23:50.948423 INFO::Fitting model to feature number 866, F897
## 2024-05-01 19:23:50.956874 INFO::Fitting model to feature number 867, F898
## 2024-05-01 19:23:50.965267 INFO::Fitting model to feature number 868, F899
## 2024-05-01 19:23:50.97367 INFO::Fitting model to feature number 869, F900
## 2024-05-01 19:23:51.200758 INFO::Counting total values for each feature
## 2024-05-01 19:23:51.350124 INFO::Writing filtered data to file Macarron_output/maaslin2_results/features/filtered_data.tsv
## 2024-05-01 19:23:51.735709 INFO::Writing filtered, normalized data to file Macarron_output/maaslin2_results/features/filtered_data_norm.tsv
## 2024-05-01 19:23:52.015483 INFO::Writing filtered, normalized, transformed data to file Macarron_output/maaslin2_results/features/filtered_data_norm_transformed.tsv
## 2024-05-01 19:23:52.364308 INFO::Writing residuals to file Macarron_output/maaslin2_results/fits/residuals.rds
## 2024-05-01 19:23:52.415912 INFO::Writing fitted values to file Macarron_output/maaslin2_results/fits/fitted.rds
## 2024-05-01 19:23:52.45797 INFO::Writing all results to file (ordered by increasing q-values): Macarron_output/maaslin2_results/all_results.tsv
## 2024-05-01 19:23:52.546153 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): Macarron_output/maaslin2_results/significant_results.tsv
## 2024-05-01 19:23:52.570989 INFO::Writing heatmap of significant results to file: Macarron_output/maaslin2_results/heatmap.pdf
## Initiating effect size calculations
## Calculating mean abundance in: IBD
## Calculating mean abundance in: Control
## Calculating effect size in: IBD
## Initiating prioritization
## Calculating meta-rank and prioritizing metabolic features
## 2024-05-01 19:23:53.095338 INFO::Writing all prioritized metabolites to file: Macarron_output/prioritized_metabolites_all.csv
## 2024-05-01 19:23:53.133409 INFO::Writing characterizable prioritized metabolites to file: Macarron_output/prioritized_metabolites_characterizable.csv
## 2024-05-01 19:23:53.184037 INFO::Writing highly prioritized metabolites in IBD to file: Macarron_output/highly_prioritized_per_module_in_IBD.csv
abundances_df = read.csv(file = prism_abundances, row.names = 1) # setting features as rownames
annotations_df = read.csv(file = prism_annotations, row.names = 1) # setting features as rownames
metadata_df = read.csv(file = prism_metadata, row.names = 1) # setting samples as rownames
taxonomy_df = read.csv(file = mets_taxonomy)
# Running Macarron
prism_prioritized <- Macarron::Macarron(input_abundances = abundances_df,
input_annotations = annotations_df,
input_metadata = metadata_df,
input_taxonomy = taxonomy_df)
The Macarron::Macarron()
function is a wrapper for the Macarron framework. Users can also apply individual functions on the input dataframes to achieve same results as the wrapper with the added benefit of storing output from each function for other analyses. There are seven steps:
# Step 1: Storing input data in a summarized experiment object
prism_mbx <- prepInput(input_abundances = abundances_df,
input_annotations = annotations_df,
input_metadata = metadata_df)
# Step 2: Creating a distance matrix from pairwise correlations in abundances of metabolic features
prism_w <- makeDisMat(se = prism_mbx)
# Step 3: Finding covariance modules
prism_modules <- findMacMod(se = prism_mbx,
w = prism_w,
input_taxonomy = taxonomy_df)
# The output is a list containing two dataframes- module assignments and measures of success
# if evaluateMOS=TRUE. To write modules to a separate dataframe, do:
prism_module_assignments <- prism_modules[[1]]
prism_modules_mos <- prism_modules[[2]]
# Step 4: Calculating AVA
prism_ava <- calAVA(se = prism_mbx,
mod.assn = prism_modules)
# Step 5: Calculating q-value
prism_qval <- calQval(se = prism_mbx,
mod.assn = prism_modules)
# Step 6: Calculating effect size
prism_es <- calES(se = prism_mbx,
mac.qval = prism_qval)
# Step 7: Prioritizing metabolic features
prism_prioritized <- prioritize(se = prism_mbx,
mod.assn = prism_modules,
mac.ava = prism_ava,
mac.qval = prism_qval,
mac.es = prism_es)
# The output is a list containing two dataframes- all prioritized metabolic features and
# only characterizable metabolic features.
all_prioritized <- prism_prioritized[[1]]
char_prioritized <- prism_prioritized[[2]]
# Step 8 (optional): View only the highly prioritized metabolic features in each module
prism_highly_prioritized <- showBest(prism_prioritized)
Session info from running the demo in R can be displayed with the following command.
sessionInfo()
## R version 4.4.0 RC (2024-04-16 r86468 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Macarron_1.9.0 SummarizedExperiment_1.35.0
## [3] Biobase_2.65.0 GenomicRanges_1.57.0
## [5] GenomeInfoDb_1.41.0 IRanges_2.39.0
## [7] S4Vectors_0.43.0 BiocGenerics_0.51.0
## [9] MatrixGenerics_1.17.0 matrixStats_1.3.0
## [11] BiocStyle_2.33.0
##
## loaded via a namespace (and not attached):
## [1] mnormt_2.1.1 DBI_1.2.2 pbapply_1.7-2
## [4] gridExtra_2.3 rlang_1.1.3 magrittr_2.0.3
## [7] compiler_4.4.0 RSQLite_2.3.6 png_0.1-8
## [10] vctrs_0.6.5 stringr_1.5.1 pkgconfig_2.0.3
## [13] crayon_1.5.2 fastmap_1.1.1 backports_1.4.1
## [16] XVector_0.45.0 utf8_1.2.4 rmarkdown_2.26
## [19] preprocessCore_1.67.0 UCSC.utils_1.1.0 bit_4.0.5
## [22] xfun_0.43 zlibbioc_1.51.0 cachem_1.0.8
## [25] jsonlite_1.8.8 blob_1.2.4 DelayedArray_0.31.0
## [28] BiocParallel_1.39.0 psych_2.4.3 Maaslin2_1.19.0
## [31] parallel_4.4.0 cluster_2.1.6 biglm_0.9-2.1
## [34] R6_2.5.1 RColorBrewer_1.1-3 stringi_1.8.3
## [37] bslib_0.7.0 rpart_4.1.23 jquerylib_0.1.4
## [40] Rcpp_1.0.12 bookdown_0.39 iterators_1.0.14
## [43] knitr_1.46 WGCNA_1.72-5 base64enc_0.1-3
## [46] Matrix_1.7-0 splines_4.4.0 nnet_7.3-19
## [49] tidyselect_1.2.1 rstudioapi_0.16.0 abind_1.4-5
## [52] yaml_2.3.8 doParallel_1.0.17 codetools_0.2-20
## [55] plyr_1.8.9 lattice_0.22-6 tibble_3.2.1
## [58] withr_3.0.0 KEGGREST_1.45.0 evaluate_0.23
## [61] foreign_0.8-86 survival_3.6-4 getopt_1.20.4
## [64] Biostrings_2.73.0 pillar_1.9.0 BiocManager_1.30.22
## [67] checkmate_2.3.1 foreach_1.5.2 pcaPP_2.0-4
## [70] generics_0.1.3 ggplot2_3.5.1 munsell_0.5.1
## [73] scales_1.3.0 glue_1.7.0 pheatmap_1.0.12
## [76] Hmisc_5.1-2 tools_4.4.0 robustbase_0.99-2
## [79] data.table_1.15.4 mvtnorm_1.2-4 fastcluster_1.2.6
## [82] grid_4.4.0 optparse_1.7.5 impute_1.79.0
## [85] AnnotationDbi_1.67.0 colorspace_2.1-0 nlme_3.1-164
## [88] GenomeInfoDbData_1.2.12 htmlTable_2.4.2 Formula_1.2-5
## [91] cli_3.6.2 fansi_1.0.6 S4Arrays_1.5.0
## [94] dplyr_1.1.4 DEoptimR_1.1-3 gtable_0.3.5
## [97] hash_2.2.6.3 logging_0.10-108 dynamicTreeCut_1.63-1
## [100] sass_0.4.9 digest_0.6.35 SparseArray_1.5.0
## [103] htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.8.1
## [106] lifecycle_1.0.4 httr_1.4.7 GO.db_3.19.1
## [109] bit64_4.0.5
The input taxonomy dataframe can be generated using the input metabolic features annotation dataframe using Macarron::decorateID()
. This function annotates an HMDB ID or a PubChem CID with the chemical class and subclass of the metabolite.
taxonomy_df <- decorateID(input_annotations = annotations_df)
write.csv(taxonomy_df, file="demo_taxonomy.csv", row.names = FALSE)
A record of all chosen parameters and steps that were followed during execution.
This file provides information about the properties of covariance modules used in the analysis. By default, modules are generated using a minimum module size (MMS) (argument: min_module_size
) equal to cube root of the total number of prevalent metabolic features. Macarron evaluates 9 measures of success (MOS) that collectively capture the “correctness” and chemical homogeneity of the modules. The MOS are as follows:
This folder contains the Maaslin2 log file (maaslin2.log), significant associations found by Maaslin2 (significant_results.tsv) and the linear model residuals file (residuals.rds). For more information, see Maaslin2.
Ideally, at least 50% metabolic features must be retained after prevalence filtering. By default, Macarron uses the union of metabolic features observed (non-zero abundance) in at least 70% samples of any phenotype for further analysis. This prevalence threshold may be high for some metabolomics datasets and can be changed using the min_prevalence
argument.
prism_prioritized <- Macarron::Macarron(input_abundances = abundances_df,
input_annotations = annotations_df,
input_metadata = metadata_df,
input_taxonomy = taxonomy_df,
min_prevalence = 0.5)
# or
prism_w <- makeDisMat(se = prism_mbx,
min_prevalence = 0.5)
By default, cube root of the total number of prevalent features is used as the minimum module size (MMS) (argument: min_module_size
) for module detection and generation. We expect this to work for most real world datasets. To determine if the modules are optimal for further analysis, Macarron evaluates several measures of success (MOS) as described above. In addition to evaluating MOS for modules generated using the default MMS, Macarron also evaluates MOS for MMS values that are larger (MMS+5, MMS+10) and smaller (MMS-5, MMS-10) than the default MMS. If you find that the MOS improve with larger or smaller MMS, you may change the default accordingly. For more details about module detection, please see WGCNA
and dynamicTreeCut
.
# See MOS of modules generated using default
prism_modules <- findMacMod(se = prism_mbx,
w = prism_w,
input_taxonomy = taxonomy_df)
prism_modules_mos <- prism_modules[[2]]
View(prism_modules_mos)
# Change MMS
prism_modules <- findMacMod(se = prism_mbx,
w = prism_w,
input_taxonomy = taxonomy_df,
min_module_size = 10)
Macarron uses Maaslin2 for determining the q-value of differential abundance in a phenotype of interest. For default execution, the phenotype of interest must be a category in column 1 of the metadata dataframe e.g. IBD in diagnosis in the demo. This is also the column that is picked by the metadata_variable
argument for identifying the main phenotypes/conditions in any dataset (see Macarron.log file). Further, in the default execution, all columns in the metadata table are considered as fixed effects and the alphabetically first categorical variable in each covariate with two categories is considered as the reference. Maaslin2 requires reference categories to be explicitly defined for all categorical metadata with more than two categories.
Defaults can be changed with the arguments fixed_effects
, random_effects
and reference
. In the demo example, fixed effects
and reference
can be defined as follows:
prism_qval <- calQval(se = prism_mbx,
mod.assn = prism_modules,
metadata_variable = "diagnosis",
fixed_effects = c("diagnosis","age","antibiotics"),
reference = c("diagnosis,Control";"antibiotics,No"))
The package source contains a script MacarronCMD.R
in inst/scripts
to invoke Macarron in the command line using Rscript.
The inst/scripts
folder also contains a README file that comprehensively documents the usage of the script.