calTMB | R Documentation |
Calculate Tumor Mutational Burden (TMB) in specific regions.
calTMB(
maf,
bedFile = NULL,
bedHeader = FALSE,
assay = "MSK-v3",
genelist = NULL,
mutType = "nonsynonymous",
bedFilter = TRUE
)
maf |
An MAF data frame, generated by |
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. |
A TMB value.
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"))
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