diff --git a/R/VCF_to_catalog_functions.R b/R/VCF_to_catalog_functions.R index 31615462..9112e219 100644 --- a/R/VCF_to_catalog_functions.R +++ b/R/VCF_to_catalog_functions.R @@ -173,7 +173,7 @@ GetStrelkaVAF <-function(vcf) { return(vaf) } -#' Read in the data lines of a Variant Call Format (VCF) file created by MuTect +#' Read in the data lines of a Variant Call Format (VCF) file created by Mutect #' #' @importFrom utils read.csv #' @@ -224,7 +224,7 @@ MakeDataFrameFromMutectVCF <- function(file) { } #' Read in the data lines of a Variant Call Format (VCF) file created by -#' MuTect +#' Mutect #' #' @importFrom utils read.csv #' diff --git a/data-raw/vcf-investigation.R b/data-raw/vcf-investigation.R new file mode 100644 index 00000000..d28deeac --- /dev/null +++ b/data-raw/vcf-investigation.R @@ -0,0 +1,11 @@ + +df <- MakeDataFrameFromMutectVCF( + "../OTA_vcf/0-5mM-OTA-S9-1_S7.bam.recal_calls.vcf") +dt <- data.table(df) +dt1 <- dt[nchar(REF) >= 2 & nchar(ALT) >= 2] +View(dt1) + +dt$VAF <- GetMutectVAF(dt) +dt.SBS <- dt[nchar(REF) == 1 & nchar(ALT) == 1] +split.vcf <- SplitStrelkaSBSVCF(dt.SBS) +View(split.vcf$DBS.vcf) diff --git a/inst/WORDLIST b/inst/WORDLIST index a4dc0eeb..fbb310ba 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -71,7 +71,6 @@ microhomology Mmusculus mutect Mutect -MuTect NN nucleotides opar diff --git a/man/MakeDataFrameFromMutectVCF.Rd b/man/MakeDataFrameFromMutectVCF.Rd index 62bf8e1e..78ac4651 100644 --- a/man/MakeDataFrameFromMutectVCF.Rd +++ b/man/MakeDataFrameFromMutectVCF.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/VCF_to_catalog_functions.R \name{MakeDataFrameFromMutectVCF} \alias{MakeDataFrameFromMutectVCF} -\title{Read in the data lines of a Variant Call Format (VCF) file created by MuTect} +\title{Read in the data lines of a Variant Call Format (VCF) file created by Mutect} \usage{ MakeDataFrameFromMutectVCF(file) } @@ -13,6 +13,6 @@ MakeDataFrameFromMutectVCF(file) A data frame storing mutation records of a VCF file. } \description{ -Read in the data lines of a Variant Call Format (VCF) file created by MuTect +Read in the data lines of a Variant Call Format (VCF) file created by Mutect } \keyword{internal} diff --git a/man/ReadMutectVCF.Rd b/man/ReadMutectVCF.Rd index 5b603fc1..8ac31fe5 100644 --- a/man/ReadMutectVCF.Rd +++ b/man/ReadMutectVCF.Rd @@ -3,7 +3,7 @@ \name{ReadMutectVCF} \alias{ReadMutectVCF} \title{Read in the data lines of a Variant Call Format (VCF) file created by - MuTect} + Mutect} \usage{ ReadMutectVCF(file) } @@ -15,6 +15,6 @@ A data frame storing mutation records of a VCF file with VAFs added. } \description{ Read in the data lines of a Variant Call Format (VCF) file created by - MuTect + Mutect } \keyword{internal}