performGISTIC2: Detect genes under selection by focal amplification/deletion...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

This can take anywhere between 30 min. up to several hours depending on the number of samples. If you have previously ran GISTIC, use the importGISTIC2 function to import and clean the data.

Usage

performGISTIC2(
  regions,
  outputFolder,
  gisticPath = "/mnt/onco0002/repository/software/GISTIC2/gistic2",
 
    gisticParameters = "-genegistic 1 -gcm extreme -maxseg 4000 -broad 1 -brlen 0.98 -conf 0.95 -rx 0 -cap 3 -saveseg 0 -armpeel 1 -smallmem 0 -res 0.01 -ta 0.3 -td 0.3 -savedata 0 -savegene 1 -qvt 0.1 -twoside 0",
 
    gisticAnno = "/mnt/onco0002/repository/software/GISTIC2/refgenefiles/hg19.UCSC.add_miR.140312.refgene.mat"
)

Arguments

regions	(GRanges): GRanges of CN segments with the following columns: sample, copyNumber, bafCount, sex.
outputFolder	(character): Path to output folder of GISTIC2 results.
gisticPath	(character): Path to gistic2 shell script.
gisticParameters	(character): Optional parameters given to gistic2. See online documentation for options.
gisticAnno	(character): Path to which genome annotation GISTIC should use? Stored in /mnt/data/ccbc_environment/software/general/GISTIC2_2.0.23/

Value

(list) GISTIC

Author(s)

Job van Riet [e-mail]

Examples

	gisticOutput <- R2CPCT::performGISTIC2(regions = data.Cohort$copyNumbers)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.