mutSelection: mutSelection

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

mutSelection

Description

Select candidate variants for cancer research.

Usage

mutSelection(
  maf,
  dbVAF = 0.01,
  ExAC = TRUE,
  Genomesprojects1000 = TRUE,
  ESP6500 = TRUE,
  gnomAD = TRUE,
  dbSNP = FALSE,
  keepCOSMIC = TRUE,
  keepType = "exonic",
  bedFile = NULL,
  bedHeader = FALSE,
  bedFilter = TRUE,
  progressbar = TRUE,
  verbose = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
dbVAF	Threshold of VAF of certain population for variants in database. Default: 0.01
ExAC	Whether to filter variants listed in ExAC with VAF higher than cutoff(set in VAF parameter). Default: TRUE.
Genomesprojects1000	Whether to filter variants listed in Genomesprojects1000 with VAF higher than cutoff(set in VAF parameter). Default: TRUE.
ESP6500	Whether to filter variants listed in ESP6500 with VAF higher than cutoff(set in VAF parameter). Default: TRUE.
gnomAD	Whether to filter variants listed in gnomAD with VAF higher than cutoff(set in VAF parameter). Default: TRUE.
dbSNP	Whether to filter variants listed in dbSNP. Default: FALSE.
keepCOSMIC	Whether to keep variants in COSMIC even they have are present in germline database. Default: TRUE.
keepType	A group of variant classifications will be kept, including 'exonic', 'nonsynonymous' and 'all'. Default: 'exonic'.
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.
bedFilter	Whether to filter the information in bed file or not, which only leaves segments in Chr1-Ch22, ChrX and ChrY. Default: TRUE
progressbar	Whether to show progress bar when running this function Default: TRUE
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame with variants after selection.

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf", package="CaMutQC"))
mafF <- mutSelection(maf)

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