mutFilterCom | R Documentation |
Apply common filtering strategies on a MAF data frame.
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
)
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 |
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. Note: CaMutQC uses unfiltered maf to calculate TMB value. |
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. |
An MAF data frame after common strategy filtration
A filter report in HTML format
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)
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