compareCCF {MesKit} | R Documentation |
Compare the CCF between samples/tumor pairs This function requires CCF for clustering
compareCCF( maf, patient.id = NULL, min.ccf = 0, pairByTumor = FALSE, use.tumorSampleLabel = FALSE, ... )
maf |
Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
min.ccf |
The minimum value of CCF. Default 0. |
pairByTumor |
Pair by tumor types in each patients. Default FALSE. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
... |
Other options passed to |
a result list of CCF comparing between samples/tumor pairs
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, ccfFile=ccf.File, refBuild="hg19") compareCCF(maf)