subMaf {MesKit} | R Documentation |
Subset Maf object
subMaf( maf, mafObj = FALSE, patient.id = NULL, geneList = NULL, chrSilent = NULL, mutType = "All", use.indel = TRUE, min.vaf = 0, max.vaf = 1, min.average.vaf = 0, min.ccf = 0, min.ref.depth = 0, min.alt.depth = 0, min.total.depth = 0, clonalStatus = NULL, use.adjVAF = FALSE, use.tumorSampleLabel = FALSE )
maf |
Maf or MafList object generated by |
mafObj |
return Maf class. (Default: FALSE). |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
geneList |
A list of genes to restrict the analysis. Default NULL. |
chrSilent |
Chromosomes excluded in the analysis. e.g, 1, 2, X, Y. Default NULL. |
mutType |
Select Proper variant classification you need. Default "All". Option: "nonSyn". |
use.indel |
Logical value. Whether to use INDELs besides somatic SNVs. (Default: TRUE). |
min.vaf |
The minimum VAF for filtering variants. Default 0. |
max.vaf |
The maximum VAF for filtering variants. Default 1. |
min.average.vaf |
The minimum tumor average VAF for filtering variants. Default 0. |
min.ccf |
The minimum CCF for filtering variants. Default NULL. |
min.ref.depth |
The minimum reference allele depth for filtering variants. Default 0. |
min.alt.depth |
The minimum alteratation allele depth for filtering variants. Default 0. |
min.total.depth |
The minimum total allele depth for filtering variants. Default 0. |
clonalStatus |
Subset by clonal status. Default NULL. Option: "Clonal","Subclonal". |
use.adjVAF |
Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
Maf object or Maf data.
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") maf_data <- subMaf(maf)