mutFilterRef: mutFilterRef

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

mutFilterRef

Description

Use the same filtering strategies that a specific study used, or top-rated strategies shared by users.

Usage

mutFilterRef(
  maf,
  reference,
  PONfile,
  PONformat = "vcf",
  tumorDP = 0,
  normalDP = 0,
  tumorAD = 0,
  normalAD = Inf,
  VAF = 0,
  VAFratio = 0,
  SBmethod = "SOR",
  SBscore = Inf,
  maxIndelLen = Inf,
  minInterval = 0,
  tagFILTER = NULL,
  dbVAF = 0.01,
  ExAC = FALSE,
  Genomesprojects1000 = FALSE,
  ESP6500 = FALSE,
  gnomAD = FALSE,
  dbSNP = FALSE,
  keepCOSMIC = FALSE,
  keepType = "all",
  bedFile = NULL,
  bedFilter = TRUE,
  mutFilter = FALSE,
  selectCols = FALSE,
  report = TRUE,
  reportFile = "FilterReport.html",
  reportDir = "./",
  TMB = FALSE,
  progressbar = TRUE,
  codelog = FALSE,
  codelogFile = "mutFilterCom.log",
  verbose = TRUE
)

Arguments

maf	An MAF data frame.
reference	A specific study whose filtering strategies need to be referred to. Format: "Last_name_of_the_first_author_et_al-Journal-Year-Cancer_type" Options are: "Haraldsdottir_et_al-Gastroenterology-2014-UCEC", "Cherniack_et_al-Cancer_Cell-2017-UCS", "Mason_et_al-Leukemia-2015-LCML", "Gerlinger_et_al-Engl_J_Med-2012-KIRC", "Zhu_et_al-Nat_Commun-2020-KIRP"
PONfile	Panel-of-Normals files, which can be either obtained through GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON-) or generated by users. Should have at least four columns: CHROM, POS, REF, ALT
PONformat	The format of PON file, either "vcf" or "txt". Default: "vcf"
tumorDP	Threshold of tumor total depth. Default: 0
normalDP	Threshold of normal total depth. Default: 0
tumorAD	Threshold of tumor alternative allele depth. Default: 0
normalAD	Threshold of normal alternative allele depth. Default: Inf
VAF	Threshold of VAF value. Default: 0
VAFratio	Threshold of VAF ratio (tVAF/nVAF). Default: 0
SBmethod	Method will be used to detect strand bias, including 'SOR' and 'Fisher'. Default: 'SOR'. SOR: StrandOddsRatio (https://gatk.broadinstitute.org/hc/en-us/articles/360041849111- StrandOddsRatio)
SBscore	Cutoff strand bias score used to filter variants. Default: 3
maxIndelLen	Maximum length of indel accepted to be included. Default: Inf
minInterval	Maximum length of interval between an SNV and an indel accepted to be included. Default: 0
tagFILTER	Variants with spcific tag in the FILTER column will be kept, Default: NULL
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: FALSE.
keepType	A group of variant classifications will be kept, including 'exonic', 'nonsynonymous' and 'all'. Default: 'all'.
bedFile	A file in bed format that contains region information. Default: NULL.
bedFilter	Whether to filter the information in bed file or not, which only leaves segments in Chr1-Ch22, ChrX and ChrY. Default: TRUE
mutFilter	Whether to directly return a filtered MAF data frame. If FALSE, a simulation filtration process will be run, and the original MAF data frame with tags in CaTag column, and a filter report will be returned. If TRUE, a filtered MAF data frame and a filter report will be generated. Default: FALSE
selectCols	Columns will be contained in the filtered data frame. By default (TRUE), the first 13 columns and 'Tumor_Sample_Barcode' column. Or a vector contains column names will be kept.
report	Whether to generate report automatically. Default: TRUE
reportFile	File name of the report. Default: 'FilterReport.html'
reportDir	Path to the output report file. Default: './'
TMB	Whether to calculate TMB. Default: TRUE
progressbar	Whether to show progress bar when running this function Default: TRUE
codelog	If TRUE, your code, along with the parameters you set, will be export in a log file. It will be convenient for users to repeat experiments. Default: FALSE
codelogFile	Where to store the codelog, only useful when codelog is set to TRUE. Default: "mutFilterCom.log"
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame after applied filtering strategies in another study

A filter report in HTML format

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf",package="CaMutQC"))
mafR <- mutFilterRef(maf, reference="Zhu_et_al-Nat_Commun-2020-KIRP",
PONfile=system.file("extdata","PON_test.txt", package="CaMutQC"), 
PONformat="txt", TMB=FALSE, verbose=FALSE, report=FALSE)

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