| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:49 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 684/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| evaluomeR 1.20.0 (landing page) José Antonio Bernabé-Díaz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the evaluomeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/evaluomeR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: evaluomeR |
| Version: 1.20.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings evaluomeR_1.20.0.tar.gz |
| StartedAt: 2024-05-09 07:16:09 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 07:21:18 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 308.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: evaluomeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings evaluomeR_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/evaluomeR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘evaluomeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘evaluomeR’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
'randomForest', 'flexmix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘evaluomeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘kableExtra’
All declared Imports should be used.
Packages in Depends field not imported from:
‘flexmix’ ‘randomForest’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flemixModel: no visible global function definition for ‘FLXMRglm’
flemixModel: no visible global function definition for ‘stepFlexmix’
flemixModel: no visible global function definition for ‘getModel’
globalMetric: no visible global function definition for ‘prior’
metrics_pca: no visible global function definition for ‘prcomp’
metrics_randomforest: no visible global function definition for
‘randomForest’
metrics_randomforest: no visible global function definition for ‘head’
speccCBI: no visible global function definition for ‘specc’
Undefined global functions or variables:
FLXMRglm getModel head prcomp prior randomForest specc stepFlexmix
Consider adding
importFrom("stats", "prcomp")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testAll.R’
Running ‘testAnalysis.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/evaluomeR.Rcheck/00check.log’
for details.
evaluomeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL evaluomeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘evaluomeR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: evaluomeR *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (evaluomeR)
evaluomeR.Rcheck/tests/testAll.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Attaching package: 'randomForest'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: flexmix
Loading required package: lattice
>
> data("rnaMetrics")
>
> dataFrame <- stability(data=rnaMetrics, k=4, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 4
> dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,4), bs=20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
> assay(dataFrame)
Metric Mean_stability_k_2 Mean_stability_k_3 Mean_stability_k_4
[1,] "RIN" "0.825833333333333" "0.778412698412698" "0.69625"
[2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> # Metric Mean_stability_k_2 Mean_stability_k_3 Mean_stability_k_4
> # [1,] "RIN" "0.825833333333333" "0.778412698412698" "0.69625"
> # [2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> dataFrame <- stabilitySet(data=rnaMetrics, k.set=c(2,3,4), bs=20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
>
> dataFrame <- quality(data=rnaMetrics, cbi="kmeans", k=3, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Processing metric: DegFact(2)
Calculation of k = 3
> assay(dataFrame)
Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
[1,] "RIN" "0.420502645502646" "0.724044583696066" "0.68338517747747"
[2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
[1,] "0.627829396038413" "4" "4" "8"
[2,] "0.737191191352892" "8" "5" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
> # [1,] "RIN" "0.420502645502646" "0.724044583696066" "0.68338517747747"
> # [2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
> # Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # [1,] "0.627829396038413" "4" "4" "8"
> # [2,] "0.737191191352892" "8" "5" "3"
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,4), seed = 20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
> assay(getDataQualityRange(dataFrame, 2))
Metric Cluster_1_SilScore Cluster_2_SilScore Avg_Silhouette_Width
1 "RIN" "0.583166775069983" "0.619872562681118" "0.608402004052639"
2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136"
Cluster_1_Size Cluster_2_Size
1 "5" "11"
2 "13" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Avg_Silhouette_Width Cluster_1_Size
> # 1 "RIN" "0.583166775069983" "0.619872562681118" "0.608402004052639" "5"
> # 2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136" "13"
> # Cluster_2_Size
> # 1 "11"
> # 2 "3"
> assay(getDataQualityRange(dataFrame, 4))
Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
1 "RIN" "0.420502645502646" "0.674226581940152" "0.433333333333333"
2 "DegFact" "0.759196481622952" "0.59496499852177" "0.600198799385732"
Cluster_4_SilScore Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size
1 "0.348714574898785" "0.463905611516569" "4" "4"
2 "0.521618857725795" "0.634170498361632" "5" "3"
Cluster_3_Size Cluster_4_Size
1 "3" "5"
2 "5" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
> # 1 "RIN" "0.420502645502646" "0.674226581940152" "0.433333333333333"
> # 2 "DegFact" "0.759196481622952" "0.59496499852177" "0.600198799385732"
> # Cluster_4_SilScore Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # 1 "0.348714574898785" "0.463905611516569" "4" "4" "3"
> # 2 "0.521618857725795" "0.634170498361632" "5" "3" "5"
> # Cluster_4_Size
> # 1 "5"
> # 2 "3"
> dataFrame1 <- qualitySet(data=rnaMetrics, k.set=c(2,3,4), getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
>
>
> dataFrame <- metricsCorrelations(data=rnaMetrics, getImages = FALSE, margins = c(4,4,11,10))
Data loaded.
Number of rows: 16
Number of columns: 3
> assay(dataFrame, 1)
RIN DegFact
RIN 1.0000000 -0.9744685
DegFact -0.9744685 1.0000000
>
>
> dataFrame <- stability(data=rnaMetrics, cbi="kmeans", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara_pam", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="hclust", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk_pam", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
>
> # Supported CBIs:
> evaluomeRSupportedCBI()
[1] "kmeans" "clara" "clara_pam" "hclust" "pamk" "pamk_pam"
>
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,10), getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
Calculation of k = 6
Calculation of k = 7
Calculation of k = 8
Calculation of k = 9
Calculation of k = 10
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
Calculation of k = 6
Calculation of k = 7
Calculation of k = 8
Calculation of k = 9
Calculation of k = 10
> dataFrame
ExperimentList class object of length 9:
[1] k_2: SummarizedExperiment with 2 rows and 6 columns
[2] k_3: SummarizedExperiment with 2 rows and 8 columns
[3] k_4: SummarizedExperiment with 2 rows and 10 columns
[4] k_5: SummarizedExperiment with 2 rows and 12 columns
[5] k_6: SummarizedExperiment with 2 rows and 14 columns
[6] k_7: SummarizedExperiment with 2 rows and 16 columns
[7] k_8: SummarizedExperiment with 2 rows and 18 columns
[8] k_9: SummarizedExperiment with 2 rows and 20 columns
[9] k_10: SummarizedExperiment with 2 rows and 22 columns
>
> #dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,8), bs=20, getImages = FALSE)
> #assay(dataFrame)
>
> proc.time()
user system elapsed
14.782 0.539 15.344
evaluomeR.Rcheck/tests/testAnalysis.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Attaching package: 'randomForest'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: flexmix
Loading required package: lattice
>
> data("rnaMetrics")
> plotMetricsMinMax(rnaMetrics)
There were 17 warnings (use warnings() to see them)
> plotMetricsBoxplot(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead.
2: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead.
> cluster = plotMetricsCluster(ontMetrics, scale = TRUE)
> plotMetricsViolin(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead.
2: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead.
3: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead.
4: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead.
>
> stabilityData <- stabilityRange(data=rnaMetrics, k.range=c(3,4), bs=20, getImages = FALSE, seed=100)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 3
Calculation of k = 4
> qualityData <- qualityRange(data=rnaMetrics, k.range=c(3,4), getImages = FALSE, seed=100)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 3
Calculation of k = 4
>
> kOptTable <- getOptimalKValue(stabilityData, qualityData, k.range=c(3,4))
Processing metric: RIN
Maximum stability and quality values matches the same K value: '3'
Processing metric: DegFact
Maximum stability and quality values matches the same K value: '3'
> kOptTable
Metric Stability_max_k Stability_max_k_stab Stability_max_k_qual
1 RIN 3 0.8901389 0.6278294
2 DegFact 3 1.0000000 0.7371912
Quality_max_k Quality_max_k_stab Quality_max_k_qual Global_optimal_k
1 3 0.8901389 0.6278294 3
2 3 1.0000000 0.7371912 3
>
>
> df = assay(rnaMetrics)
> k.vector1=rep(5,length(colnames(df))-1)
> k.vector2=rep(2,length(colnames(df))-1)
>
> plotMetricsClusterComparison(rnaMetrics, k.vector1=k.vector1, k.vector2=k.vector2)
> plotMetricsClusterComparison(rnaMetrics, k.vector1=3, k.vector2=c(2,5))
>
>
> proc.time()
user system elapsed
13.820 0.495 14.325
evaluomeR.Rcheck/evaluomeR-Ex.timings
| name | user | system | elapsed | |
| evaluomeRSupportedCBI | 0 | 0 | 0 | |
| getDataQualityRange | 0.579 | 0.004 | 0.585 | |
| getOptimalKValue | 0.438 | 0.016 | 0.455 | |
| globalMetric | 1.655 | 0.015 | 1.676 | |
| metricsCorrelations | 0.052 | 0.000 | 0.052 | |
| plotMetricsBoxplot | 0.883 | 0.008 | 0.894 | |
| plotMetricsCluster | 0.203 | 0.000 | 0.204 | |
| plotMetricsClusterComparison | 1.265 | 0.075 | 1.344 | |
| plotMetricsMinMax | 0.799 | 0.012 | 0.813 | |
| plotMetricsViolin | 1.113 | 0.048 | 1.165 | |
| quality | 0.398 | 0.028 | 0.427 | |
| qualityRange | 0.310 | 0.012 | 0.323 | |
| qualitySet | 0.071 | 0.000 | 0.071 | |
| stability | 3.124 | 0.048 | 3.179 | |
| stabilityRange | 3.642 | 0.032 | 3.683 | |
| stabilitySet | 0.518 | 0.000 | 0.520 | |