readMaf {MesKit} | R Documentation |
Read tab delimited MAF (can be plain text or *.gz compressed) file along with sample information file.
readMaf( mafFile, clinicalFile, ccfFile = NULL, adjusted.VAF = FALSE, nonSyn.vc = NULL, use.indel.ccf = FALSE, ccf.conf.level = 0.95, refBuild = "hg19" )
mafFile |
A tab delimited MAF file (plain text or *.gz compressed). Required. |
clinicalFile |
A clinical data file includes Tumor_Sample_Barcode, Tumor_ID, Patient_ID. Tumor_Sample_Label is optional. Default NULL. |
ccfFile |
A CCF file of somatic mutations. Default NULL. |
adjusted.VAF |
Whether adjusted VAF is included in mafFile. Default FALSE. |
nonSyn.vc |
List of Variant classifications which are considered as non-silent. Default NULL, use Variant Classifications with "Frame_Shift_Del","Frame_Shift_Ins","Splice_Site","Translation_Start_Site","Nonsense_Mutation","Nonstop_Mutation","In_Frame_Del","In_Frame_Ins","Missense_Mutation" |
use.indel.ccf |
Whether include indels in ccfFile. Default FALSE. |
ccf.conf.level |
The confidence level of CCF to identify clonal or subclonal. Only works when "CCF_std" or "CCF_CI_high" is provided in ccfFile. Default 0.95. |
refBuild |
Human reference genome version. Default 'hg19'. Optional: 'hg18' or 'hg38'. |
an object of Maf or MafList.
maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit") clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit") ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit") maf <- readMaf(mafFile=maf.File,clinicalFile = clin.File, refBuild="hg19") maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")