TCGAWorkflow 1.2.0
Tiago Chedraoui Silva
| Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018) |
| URL: https://git.bioconductor.org/packages/TCGAWorkflow |
| Branch: RELEASE_3_7 |
| Last Commit: f07f804 |
| Last Changed Date: 2018-04-30 10:07:09 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R")'
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> rmarkdown::render(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")
processing file: TCGAWorkflow.Rmd
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--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
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oo Filtering results
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ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-GBM
GDCdownload will download 2 files. A total of 60.227 KB
Downloading as: Fri_May_18_08_53_28_2018.tar.gz
To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event
=> drugs: drug
=> follow_ups: follow_up
=> radiations: radiation
Parsing follow up version: follow_up_v1.0
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gbm subtype information from:doi:10.1016/j.cell.2015.12.028
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Starting GBM
trying URL 'ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19_support/CNV.hg19.bypos.111213.txt'
Content type 'unknown' length 358469 bytes (350 KB)
==================================================
Parsed with column specification:
cols(
ID = col_character(),
Chromosome = col_integer(),
Start = col_integer(),
End = col_integer(),
Flankingstart = col_integer(),
Flankingend = col_integer()
)
Loading Marker Informations
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Done
Loading Copy Number Data
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Done
Performing Data Preprocessing
Done
Computing Discontinuity Matrix
.
Done
Computing Probability Distribution
....
Done
Assessing the Significance of Observed Data
..
Done
Writing GAIA_GBM_flt.txt.igv.gistic File for Integrative Genomics Viewer (IGV) Tool
..
Done
Running Homogeneous peel-off Algorithm With Significance Threshold of 0.25 and Homogenous Threshold of 0.12
..
Done
Writing Output File 'GAIA_GBM_flt.txt' Containing the Significant Regions
File 'GAIA_GBM_flt.txt' Saved
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silent variants: 38433
Summarizing..
Gene Summary..
NOTE: Possible FLAGS among top ten genes:
Checking clinical data..
Annotation missing for below samples in MAF
Done !
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gbm subtype information from:doi:10.1016/j.cell.2015.12.028
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
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Looking for clinical data in annoatation slot of MAF..
Number of mutated samples for given genes:
Median survival..
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========================================
circlize version 0.4.3
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
in R. Bioinformatics 2014.
========================================
Note: 2 points are out of plotting region in sector 'chr17', track '4'.
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Note: 2 points are out of plotting region in sector 'chr17', track '5'.
Note: 2 points are out of plotting region in sector 'chr17', track '5'.
Note: 1 point is out of plotting region in sector 'chr17', track '5'.
Note: 1 point is out of plotting region in sector 'chr17', track '5'.
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I Need about 11 seconds for this Complete Normalization Upper Quantile [Processing 80k elements /s]
Step 1 of 4: newSeqExpressionSet ...
Step 2 of 4: withinLaneNormalization ...
Step 3 of 4: betweenLaneNormalization ...
Step 4 of 4: .quantileNormalization ...
Batch correction skipped since no factors provided
----------------------- DEA -------------------------------
there are Cond1 type LGG in 20 samples
there are Cond2 type GBM in 20 samples
there are 14477 features as miRNA or genes
I Need about 19 seconds for this DEA. [Processing 30k elements /s]
----------------------- END DEA -------------------------------
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clusterProfiler v3.8.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Attaching package: 'clusterProfiler'
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Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
'select()' returned 1:many mapping between keys and columns
Info: Downloading xml files for hsa05214, 1/1 pathways..
Info: Downloading png files for hsa05214, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.7-workflows/meat/.buildwebvig/TCGAWorkflow
Info: Writing image file hsa05214.pathview.png
Info: some node width is different from others, and hence adjusted!
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==================== DATA Summary ====================
==================== END DATA Summary ====================
==================== T test results ====================
==================== END T test results ====================
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Group1:TCGA-GBM
Group2:TCGA-LGG
Calculating the diference between the mean methylation of the groups...
Calculating the p-values of each probe...
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Loading required package: grid
========================================
ComplexHeatmap version 1.18.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://bioconductor.org/packages/ComplexHeatmap/
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
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Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
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Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
o Fetching auxiliary information
oo Fetching probes genomic information
http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds
trying URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds'
Content type 'unknown' length 18546360 bytes (17.7 MB)
==================================================
downloaded 17.7 MB
oo Fetching TSS information
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
o Mapping probes to nearest TSS
o Mapping results information
o Plotting figure
oo Adding names to genes
o Saving results
oo Saving significant results as: starburst_results.csv
oo It contains pair with changes both in the expression level of the nearest gene and in the DNA methylation level
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ChIPseeker v1.16.0 For help: https://guangchuangyu.github.io/ChIPseeker
If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
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Loading required package: ELMER.data
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Returning distal probes: 163576
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Checking samples have both DNA methylation and Gene expression and they are in the same order...
Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
=> Adding subtype information to samples
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
Creating MultiAssayExperiment
MAE saved as: mae.rda
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Get diff methylated probes
ELMER will search for probes hypomethylated in group TCGA-GBM (n:10) compared to TCGA-LGG (n:10)
Number of probes: 2936
Saving results
Number of relevant probes found: 289
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Get nearby genes
Searching for the 4 near genes
Get anti correlated probes-genes
Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------
* Filtering probes
-------------------
For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 2287 probes out of 2936
Calculating Pp (probe - gene) for all nearby genes
File created: elmer/hypo/getPair.hypo.all.pairs.statistic.csv
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Update the distance to gene to distance to the nearest TSS of the gene
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Loading object: Probes.motif.hg19.450K
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
------------------------------------
** Filtering motifs based on quality
------------------------------------
Number of enriched motifs with quality:
-----------
=> A: 15
=> B: 5
=> C: 6
=> D: 5
=> S: 0
-----------
Considering only motifs with quality from A up to DS: 31 motifs are enriched.
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Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------------------------------------------------------------------------------------------------------
** Downloading TF list from Lambert, Samuel A., et al. The human transcription factors. Cell 172.4 (2018): 650-665.
-------------------------------------------------------------------------------------------------------------------
Accessing TF families from TFClass database to indentify known potential TF
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Calculating the average methylation at all motif-adjacent probes
Performing Mann-Whitney U test
Finding potential TF and known potential TF
-----------------
** Creating plots
-----------------
TF rank plot highlighting TF in the same family (folder: elmer/hypo/TFrankPlot)
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Saving plot as: elmer/hypo/TFrankPlot/ETS1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF6_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF5_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN524_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/EGR2_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF2_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAG1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZFP82_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/GRHL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP2_HUMAN.H11MO.1.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ERG_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN341_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELK4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN467_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF14_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F3_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN331_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FEV_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF15_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF12_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/MBD2_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/EHF_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F7_HUMAN.H11MO.0.B.TFrankPlot.pdf
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Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
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output file: TCGAWorkflow.knit.md
/usr/bin/pandoc +RTS -K512m -RTS TCGAWorkflow.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output TCGAWorkflow.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.7-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --include-in-header /tmp/Rtmp12XWgf/rmarkdown-str440910792d7f.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc
pandoc-citeproc: reference sham2014statistical not found
Output created: TCGAWorkflow.html
There were 50 or more warnings (use warnings() to see the first 50)
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processing file: .buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd
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output file: .buildwebvig/TCGAWorkflow/TCGAWorkflow.R
[1] ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R"
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