mutFilterCom: mutFilterCom

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

mutFilterCom

Description

Apply common filtering strategies on a MAF data frame.

Usage

mutFilterCom(
  maf,
  PONfile,
  PONformat = "vcf",
  panel = "Customized",
  tumorDP = 20,
  normalDP = 10,
  tumorAD = 5,
  normalAD = Inf,
  VAF = 0.05,
  VAFratio = 0,
  SBmethod = "SOR",
  SBscore = 3,
  maxIndelLen = 50,
  minInterval = 10,
  tagFILTER = "PASS",
  dbVAF = 0.01,
  ExAC = TRUE,
  Genomesprojects1000 = TRUE,
  gnomAD = TRUE,
  dbSNP = FALSE,
  keepCOSMIC = TRUE,
  keepType = "exonic",
  bedFile = NULL,
  bedHeader = FALSE,
  bedFilter = TRUE,
  mutFilter = FALSE,
  ESP6500 = TRUE,
  selectCols = TRUE,
  report = TRUE,
  assay = "MSK-v3",
  genelist = NULL,
  mutType = "nonsynonymous",
  reportFile = "FilterReport.html",
  reportDir = "./",
  TMB = TRUE,
  cancerType = NULL,
  reference = NULL,
  progressbar = TRUE,
  codelog = FALSE,
  codelogFile = "mutFilterCom.log",
  verbose = TRUE
)

Arguments

maf	An MAF data frame.
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"
panel	The sequencing panel applied on the dataset. Parameters for mutFilterQual function are set differently for different panels. Default: "Customized". Options: "MSKCC", "WES".
tumorDP	Threshold of tumor total depth. Default: 20
normalDP	Threshold of normal total depth. Default: 10
tumorAD	Threshold of tumor alternative allele depth. Default: 5
normalAD	Threshold of normal alternative allele depth. Default: Inf
VAF	Threshold of VAF value. Default: 0.05
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: 50.
minInterval	Maximum length of interval between an SNV and an indel accepted to be included. Default: 10.
tagFILTER	Variants with spcific tag in the FILTER column will be kept, Default: 'PASS'.
dbVAF	Threshold of VAF value for databases. 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.
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.
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.
ESP6500	Whether to filter variants listed in ESP6500 with VAF higher than cutoff(set in VAF parameter). Default: TRUE.
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
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' and 'nonsynonymous'. Default: 'nonsynonymous'.
reportFile	File name of the report. Default: 'FilterReport.html'
reportDir	Path to the output report file. Default: './'.
TMB	Whether to calculate TMB. Default: TRUE.
cancerType	Type of cancer whose filtering parameters need to be referred to. Options are: "COADREAD", "BRCA", "LIHC", "LAML", "LCML", "UCEC", "UCS", "BLCA", "KIRC" and "KIRP"
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"
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 common strategy filtration

A filter report in HTML format

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf", package="CaMutQC"))
mafF <- mutFilterCom(maf,
PONfile=system.file("extdata", "PON_test.txt", package="CaMutQC"),
TMB=FALSE, report=FALSE, PONformat="txt", verbose=FALSE)

likelet/CaMutQC documentation built on April 3, 2024, 9:06 a.m.