subMaf: Subset Maf object

Description Usage Arguments Value Examples

View source: R/subMaf.R

Description

Subset Maf object

Usage

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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'.

min.average.adj.vaf

The minimum tumor average ajust VAF for filtering variants. Default 0.

Value

Maf object or Maf data.

Examples

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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)

MesKit documentation built on March 28, 2021, 6 p.m.