subMaf: Subset Maf object

In Niinleslie/MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

Subset Maf object

Usage

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
)

Arguments

maf	Maf or MafList object generated by readMaf function.
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'.

Value

Maf object or Maf data.

Examples

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)

Niinleslie/MesKit documentation built on Jan. 29, 2022, 10:24 a.m.