mutCluster {MesKit} | R Documentation |
Cluster mutations based on variant allele frequencies (VAFs) or cancer cell fractions (CCFs).
mutCluster( maf, patient.id = NULL, use.ccf = FALSE, segFile = NULL, withinTumor = FALSE, use.tumorSampleLabel = FALSE, ... )
maf |
Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
use.ccf |
Cluster CCF. Default FALSE. |
segFile |
The segment file. |
withinTumor |
Cluster Tumor average CCF within tumors in each patients. Default FALSE. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
... |
Other options passed to |
clustering plots of vaf
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") mutCluster(maf, patient.id = 'V402')