classifyMut {MesKit} | R Documentation |
classifyMut
classifyMut(maf, patient.id = NULL, class = "SP", classByTumor = FALSE, ...)
maf |
Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included |
class |
The class which would be represented. Default: "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS". |
classByTumor |
Logical (Default: FALSE). Classify mutations based on "Tumor_ID". |
... |
Other options passed to |
A data.frame with classification of mutations for each patient
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") classifyMut(maf, class = "SP")