calTMB: calTMB

In likelet/CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

calTMB

Description

Calculate Tumor Mutational Burden (TMB) in specific regions.

Usage

calTMB(
  maf,
  bedFile = NULL,
  bedHeader = FALSE,
  assay = "MSK-v3",
  genelist = NULL,
  mutType = "nonsynonymous",
  bedFilter = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
bedFile	A file in bed format that contains region information. Default: NULL.
bedHeader	Whether the input bed file has a header or not. Default: FALSE.
assay	Methodology and assay will be applied as a reference, including 'MSK-v3', 'MSK-v2', 'MSK-v1', 'FoundationOne', 'Pan-Cancer Panel' and 'Customized'. Default: 'MSK-v3'.
genelist	A vector of panel gene list, only useful when assay is set to 'Customized'.
mutType	A group of variant classifications that will be kept, only useful when assay is set to 'Pan-Cancer Panel' or 'Customized', including 'exonic', 'nonsynonymous'. and 'all' Default: 'nonsynonymous'.
bedFilter	Whether to filter the information in bed file or not, which only leaves segments in Chr1-Ch22, ChrX and ChrY. Default: TRUE.

Value

A TMB value.

Examples

maf <- vcfToMAF(system.file("extdata", "WES_EA_T_1_mutect2.vep.vcf",
package="CaMutQC"))
TMB_value <- calTMB(maf, bedFile=system.file("extdata/bed/panel_hg38",
"FlCDx-hg38.rds", package="CaMutQC"))

likelet/CaMutQC documentation built on Aug. 17, 2024, 4 a.m.