See instructions for snakemake pipeline
The main ichorCNA R script can also be run with even more exposed options once WIG files for read counts have been generated.
Here is an example of how to launch the R script from the command line:
Rscript ../runIchorCNA.R --libdir ../../R/ --datadir ../../inst/extdata/ \
--id tumor_sample1 --WIG results/readDepth/tumor_sample1.bin1000000.wig \
--ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 \
--includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" \
--estimateNormal True --estimatePloidy True --estimateScPrevalence True \
--scStates "c(1,3)" --centromere ../../inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt \
--exons.bed None --txnE 0.9999 --txnStrength 10000 --plotFileType png --plotYLim "c(-2,4)" \
--outDir results/ichorCNA/tumor_sample1/ > logs/ichorCNA/tumor_sample1.log 2> logs/ichorCNA/tumor_sample1.log
The list of arguments that can be passed to the script by invoking --help
:
>Rscript runIchorCNA.R --help
Usage: runIchorCNA.R [options]
Options:
-l LIBDIR, --libdir=LIBDIR
Script library path
--datadir=DATADIR
Reference wig dir path
-t WIG, --WIG=WIG
Path to tumor WIG file.
--NORMWIG=NORMWIG
Path to normal WIG file.
--normalPanel=NORMALPANEL
Median corrected depth from panel of normals
-e EXONS.BED, --exons.bed=EXONS.BED
Path to bed file containing exon regions.
--id=ID
Patient ID.
-n NORMAL, --normal=NORMAL
Initial normal contamination
--scStates=SCSTATES
Subclonal states to consider
-p PLOIDY, --ploidy=PLOIDY
Initial tumour ploidy
-m MAXCN, --maxCN=MAXCN
Total clonal CN states
--estimateNormal=ESTIMATENORMAL
Estimate normal.
--estimateScPrevalence=ESTIMATESCPREVALENCE
Estimate subclonal prevalence.
--estimatePloidy=ESTIMATEPLOIDY
Estimate tumour ploidy.
(plus more arguments)
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