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yvan edited this page May 21, 2014 · 6 revisions

SPO

linked to this issue

New procedure for creating gene panel region files for e.g. coverage calculations

  1. Molecular biologists (e.g. Tove) uses Ensembl biomart to derive a list of selected transcripts for the genes in the gene panel. A tab-separated file containing the following columns is given to a biobinformatician: chromosome, ensemblGeneStart, ensemblGeneEnd, geneSymbol, refseq, strand, band, ensemblGeneID, ensemblTranscriptID, ensemblTxStart, ensemblTxend

  2. The bioinformatician runs the script make_region_files.py, that creates three files:

    • transcripts.csv : One record per transcript with identifiers and exons. eTranscriptID, exonStarts, exonEnds)) + '\n')
    • targetRegions.bed : One record per coding exon (typically) for variantcalling.
    • coverageRegions.bed : As targetRegions.bed, but for coverage regions.

  3. The files are put in the reference repository in their own folder specific to this version of the gene panel.

The script needs as input a standard refGene file from UCSC, available for download from the UCSC table browser. The script matches the RefSeq identifiers from the biomart file with the Refseqs in the refGene file. Multiple Refseqs with the same name in the refGene file can be candidate matches. The refGene Refseq with the smallest total absolute distance in txStart and txEnd is chosen. If multiple Refseqs with the same total txStart and txEnd distance is available, the first of such Refseqs is chosen. A warning is given if the distance in txStart and/or txEnd is greater than 200 bp. (This situation often occurs, as the Ensembl transcript start/stop is different from the Refseq start/stop, but the coding exons typically lie on the exact same positions.)

The transcripts.csv file contains the following tab-separated columns: chromosome, txStart, txEnd, refseqName, 0, strand, geneSymbol, eGeneID, eTranscriptID, exonStarts, exonEnds. The exonStarts and exonEnds contain multiple comma-separated values. This file is the 'main' file describing a gene panel.

The other region files are standard BED6 files. The name column follows the convention gene__transcript__exon1 where exon count start at 1 and increase in the 5'->3' direction of the gene (i.e. strand-dependable). By default, only coding exons are used, but the numbering is according to all exons (coding/noncoding) in the refGene record. The order of apperance of the exons (not the numbering) is always in the 5'->3' direction of the forward strand (i.e. intervals are ordered left-to-right on forward strand). The names in the BED files are crucial for correct aggregation in the coverage calculation scripts.

By default, the script creates two region files, a coverageRegions.bed file using coding exons and a 'slop' of 2, and a targetRegions.bed file using coding exons and a slop of 20.

How I did it

 1. Need to adjust $PYTHONPATH to export PYTHONPATH=/Users/yvans/Home/workspace/amg ONLY!
 2. Ask The Eidi for the ENSEMBL file for brca1/2 genes use in diagnostic
 3. Save it in the working directory, mart_export_BRCA_08112013.xls
  3.1. Change the biomart file's format
  3.1.1. Need to change the the format of the file and according to Tony documentation should have these columns
   3.1.2. Clear formating, URL and others
   3.1.3. Remove

         Ensembl Genes 73  
         Homo sapiens genes GRCh37.p12

   3.1.4. Save as csv, but change field delimiter to Tabs and no Text delimiters
 4. Get the bed file
  4.1. Go To uses table http://genome.ucsc.edu/cgi-bin/hgTables?command=start
  4.2. Select track:RefSeq Genes
  4.3. output format: all fields from selected table
  4.4. Press get output
  4.5. Save the file in the working directory NM_000059_NM_007294_uscs_export
 6. Run the code

> python ../scripts/make_region_files.py --biomartfile mart_export_BRCA_08112013.csv --refgene NM_000059_NM_007294_uscs_export --genepanel HBOC
From 2 refseqNames, found total of 2 records in refGene. 0 names have duplicates.
transcripts.csv and region files written to path '.'

This produce these new files:

  • HBOC_OUS_medGen_v01_b37.codingExons.bed
  • HBOC_OUS_medGen_v01_b37.codingExons.slop
  • HBOC_OUS_medGen_v01_b37.codingExons.slop
  • HBOC_OUS_medGen_v01_b37.codingExons.slop30.bed
  • HBOC_OUS_medGen_v01_b37.codingExons.slop50.bed

06Mai2014

Follow instructions form this SPO

  1. Download tables from Veronica's email (new candidategenlist: CDG syndromer ) in /Volumes/Nor4GBExFAT/coverage/CDG_mart_export_v2_140414_verbog.xls
  2. Have a look at this issue
  3. remove the first 5 lines
  4. remove conditional formating
  5. save as csv
  6. open in TextWrangler to check, ok
  7. According to Tony, the script requires the columns in the following order for the HGMD file: HGMD_ID, Disease, Variant, Class, GeneSymbol, Chromosome, Start, End, Strand
  8. Why this have been changed??? Veronica send a ensembl file which should have this order of columns chromosome, EnsemblGeneStart, EnsemblGeneEnd, HUGO geneSymbol, refseq, strand, band, EnsemblGeneID, EnsemblTranscriptID, transcriptionStart, transcriptionEnd, entrezID.
  9. IMPORTANT the SOP should be updated because it will not work with the columns order specified in the SOP
  10. Change the file to contain only , HGMD_ID, Disease, Variant, Class, GeneSymbol, Chromosome, Start, End, Strand, The file provided by Veronica is not from the correct format
  11. Step 2 of the SOP should be skipped.....
  12. Step 3
    • py /Users/yvans/Home/workspace/amg/scripts/make_region_files.py --biomartfile=./biomartexport --refgene=./refgeneUCSC --outputdir=./ --genepanel=genepanelName --version=01 --dict=./genomeDict
Traceback (most recent call last):
  File "/Users/yvans/Home/workspace/amg/scripts/make_region_files.py", line 21, in 
    from annotation.gene import refseq
ImportError: No module named annotation.gene

* Check PYTHONPATH
* Only the export PYTHONPATH=/Users/yvans/Home/workspace/amg should be uncomented
* py /Users/yvans/Home/workspace/amg/scripts/make_region_files.py --biomartfile=./biomartexport --refgene=./refgeneUCSC --outputdir=./ --genepanel=genepanelName --version=01 --dict=./genomeDict

usage: make_region_files.py [-h] --biomartfile BIOMARTPATH --refgene
                            REFGENEPATH [--outputdir OUTPUTDIRECTORYPATH]
                            [--genepackage GENEPACKAGENAME]
                            [--version GENEPACKAGEVERSION]
make_region_files.py: error: unrecognized arguments: --genepanel=genepanelName --dict=./genomeDict

* py /Users/yvans/Home/workspace/amg/scripts/make_region_files.py --biomartfile=./CDG_mart_export_v2_140414_verbog.csv --refgene=./refgeneUCSC --outputdir=./ --genepanel=genepanelName --version=01 --dict=./genomeDict

usage: make_region_files.py [-h] --biomartfile BIOMARTPATH --refgene
                            REFGENEPATH [--outputdir OUTPUTDIRECTORYPATH]
                            [--genepackage GENEPACKAGENAME]
                            [--version GENEPACKAGEVERSION]
make_region_files.py: error: unrecognized arguments: --genepanel=genepanelName --dict=./genomeDict

* py /Users/yvans/Home/workspace/amg/scripts/make_region_files.py --biomartfile=./CDG_mart_export_v2_140414_verbog.csv --refgene=./refgeneUCSC --outputdir=./ --genepanel=CDG --version=01 --dict=./genomeDict

usage: make_region_files.py [-h] --biomartfile BIOMARTPATH --refgene
                            REFGENEPATH [--outputdir OUTPUTDIRECTORYPATH]
                            [--genepackage GENEPACKAGENAME]
                            [--version GENEPACKAGEVERSION]
make_region_files.py: error: unrecognized arguments: --genepanel=CDG --dict=./genomeDict

* I need files from the DataRepo...

08Mai2014

###Update DataRepo

  • Update DataRepo with GitHub for Mac
    • cd /Volumes/Analysis/dataDistro_r01_d01_LocalCopy/
    • /Users/yvans/Home/workspace/amg/repos/dataDistroToLocalCopy.bash -e /Volumes/refdata/dataDistro_r01_d01 /Volumes/Analysis/dataDistro_r01_d01_LocalCopy

####Run the code

py /Users/yvans/Home/workspace/amg/scripts/make_region_files.py
--biomartfile=./CDG_mart_export_v2_140414_verbog.csv
--refgene=/Volumes/Analysis/dataDistro_r01_d01_LocalCopy/b37/funcAnnot/refSeq/refGene_131119.tab 
--outputdir=./
--genepanel=CDG 
--version=01 
--dict=/Volumes/Analysis/dataDistro_r01_d01_LocalCopy/b37/genomic/gatkBundle_2.5/human_g1k_v37_decoy.dict

Some warnings

/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_006765 is far away from Ensembl txStart/stop (distances 196 and 2190)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_024105 is far away from Ensembl txStart/stop (distances 0 and 2977)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_178862 is far away from Ensembl txStart/stop (distances 209 and 1556)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_024740 is far away from Ensembl txStart/stop (distances 717 and 4089)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_033087 is far away from Ensembl txStart/stop (distances 8 and 942)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_019109 is far away from Ensembl txStart/stop (distances 10 and 1985)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
/Users/yvans/Home/workspace/amg/scripts/make_region_files.py:91: UserWarning: Note that Refseq NM_152713 is far away from Ensembl txStart/stop (distances 0 and 332)
  warnings.warn("Note that Refseq {} is far away from Ensembl txStart/stop (distances {} and {})".format(rsName, abs(rs.start-txStart), abs(rs.stop - txEnd)))
From 26 refseqNames, found total of 26 records in refGene. 0 names have duplicates.
transcripts.csv and region files written to path './'

Create hgmd.bed file

No hgmd.bed was made

Bundle all

  • mkdir CDG_OUS_medGen_v01_b37
  • mv CDG_OUS_medGen_v01_b37.* CDG_OUS_medGen_v01_b37/
  • mv CDG_mart_export_v2_140414_verbog.* CDG_OUS_medGen_v01_b37/
  • cp CDG_OUS_medGen_v01_b37/CDG_mart_export_v2_140414_verbog.xls CDG_OUS_medGen_v01_b37/Ensembl_biomart_export.xls
  • cp -r CDG_OUS_medGen_v01_b37 /Volumes/data.odin/common/clinicalGenePanels
  • cd /Volumes/data.odin/common/clinicalGenePanels/CDG_OUS_medGen_v01_b37
  • ln -s CDG_OUS_medGen_v01_b37.codingExons.slop2.bed coverageRegions.bed

Some checks

Check if the number of genes is the same in bed and csv files CDG_OUS_medGen_v01_b37 yvans$ cut -f4 CDG_OUS_medGen_v01_b37.codingExons.bed |cut -d'_' -f1|sort |uniq |grep -v "#"|wc -l; cut -f4 CDG_mart_export_v2_140414_verbog.csv |wc -l

  26
  26

Open IGV to check the .slope50 file everything seems alright.

12mai2014

Had to update some packages in R

source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade")

Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Old packages: 'boot', 'caTools', 'class', 'cluster', 'foreign', 'gdata',
  'gplots', 'gsalib', 'gtools', 'KernSmooth', 'lattice', 'MASS', 'Matrix',
  'mgcv', 'nlme', 'nnet', 'plyr', 'reshape', 'reshape2', 'rpart', 'scales',
  'spatial', 'survival'
Update all/some/none? [a/s/n]: a
also installing the dependency ‘Rcpp’

Install Gviz

biocLite("Gviz")

Installing package(s) 'Gviz'
also installing the dependencies ‘Formula’, ‘XML’, ‘zlibbioc’, ‘RCurl’, ‘DBI’, ‘RSQLite’, ‘Hmisc’, ‘IRanges’, ‘XVector’, ‘rtracklayer’, ‘biomaRt’, ‘GenomicRanges’, ‘AnnotationDbi’, ‘Biobase’, ‘BiocGenerics’, ‘GenomicFeatures’, ‘BSgenome’, ‘Biostrings’, ‘biovizBase’, ‘Rsamtools’, ‘latticeExtra’

Install Hmisc

install.packages("Hmisc")

Install Ghostscript

pcus572:CDG_OUS_medGen_v01_b37 yvans$ sudo port install ghostscript

Then run the multisample.py script


Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000109502-KIT-AI50Mbv5.131009_7001448_0224_BC2G61ACXX/060_delivery/Sample_Diag-excap17-13000109502-KIT-AI50Mbv5.131009_7001448_0224_BC2G61ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000109502 (1/18)

Sample 13000109502 : Getting coveragePerBasepair

Sample 13000109502 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000055302-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX/060_delivery/Sample_Diag-excap17-13000055302-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000055302 (2/18)

Sample 13000055302 : Getting coveragePerBasepair

Sample 13000055302 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000109502-KIT-AI50Mbv5.131009_7001448_0224_BC2G61ACXX/060_delivery/Sample_Diag-excap17-13000109502-KIT-AI50Mbv5.131009_7001448_0224_BC2G61ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000109502 (3/18)

Sample 13000109502 : Getting coveragePerBasepair

Sample 13000109502 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000703501-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX/060_delivery/Sample_Diag-excap17-13000703501-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000703501 (4/18)

Sample 13000703501 : Getting coveragePerBasepair

Sample 13000703501 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000766100-KIT-

AI50Mbv5.131009_7001448_0223_AC2G2UACXX/060_delivery/Sample_Diag-excap17-13000766100-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000766100 (5/18)

Sample 13000766100 : Getting coveragePerBasepair

Sample 13000766100 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap17-13000766800-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX/060_delivery/Sample_Diag-excap17-13000766800-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000766800 (6/18)

Sample 13000766800 : Getting coveragePerBasepair

Sample 13000766800 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap18-13000427703-KIT-AI50Mbv5.131127_D00132_0057_BC36K4ACXX/060_delivery/Sample_Diag-excap18-13000427703-KIT-AI50Mbv5.131127_D00132_0057_BC36K4ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000427703 (7/18)

Sample 13000427703 : Getting coveragePerBasepair

Sample 13000427703 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/Bindevev/Sample_Diag-excap18-13000630901-KIT-AI50Mbv5.131127_D00132_0057_BC36K4ACXX/060_delivery/Sample_Diag-excap18-13000630901-KIT-AI50Mbv5.131127_D00132_0057_BC36K4ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000630901 (8/18)

Sample 13000630901 : Getting coveragePerBasepair

Sample 13000630901 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap17-13000657400-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX/060_delivery/Sample_Diag-excap17-13000657400-KIT-AI50Mbv5.131009_7001448_0223_AC2G2UACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000657400 (9/18)

Sample 13000657400 : Getting coveragePerBasepair

Sample 13000657400 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-D09-3034-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-D09-3034-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName D09 (10/18)

Sample D09 : Getting coveragePerBasepair

Sample D09 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000644201-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000644201-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000644201 (11/18)

Sample 13000644201 : Getting coveragePerBasepair

Sample 13000644201 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000601601-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000601601-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000601601 (12/18)

Sample 13000601601 : Getting coveragePerBasepair

Sample 13000601601 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000526402-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000526402-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000526402 (13/18)

Sample 13000526402 : Getting coveragePerBasepair

Sample 13000526402 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000242803-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000242803-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000242803 (14/18)

Sample 13000242803 : Getting coveragePerBasepair

Sample 13000242803 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000550100-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000550100-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000550100 (15/18)

Sample 13000550100 : Getting coveragePerBasepair

Sample 13000550100 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000435202-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000435202-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000435202 (16/18)

Sample 13000435202 : Getting coveragePerBasepair

Sample 13000435202 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000413500-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000413500-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000413500 (17/18)

Sample 13000413500 : Getting coveragePerBasepair
Sample 13000413500 : Calculating regions with low coverage

Calling coverage_qc.py on bamPath /Volumes/data1.odin/001_exome/diagnosticSamples/EE/Sample_Diag-excap16-13000378300-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX/060_delivery/Sample_Diag-excap16-13000378300-KIT-AI50Mbv5.130906_SN586_0177_AC2730ACXX.all.realigned.markDup.baseQreCali.bam  sampleName 13000378300 (18/18)

Sample 13000378300 : Getting coveragePerBasepair

Sample 13000378300 : Calculating regions with low coverage

Then run the R script

pcus572:CDG_OUS_medGen_v01_b37 yvans$ Rscript /Users/yvans/Home/workspace/amg/variantcalling/qc/coverage/analysis/coverage_analysis.R

Loading required package: ggplot2
Loading required package: methods
Loading required package: Gviz
Loading required package: grid
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: splines
Loading required package: Formula

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: gtools
null device
          1
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
    7.0    91.5   122.0   144.0   165.0  1621.0
null device
          1
ALG6  Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:Hmisc’:

    combine

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

ALG1  ALG13  STT3B  DPM1  null device
          1

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