Minor documentation updates and a temporary test script

steverozen · Jul 18, 2019 · 709e75c · 709e75c
1 parent 4cd31ad
commit 709e75c
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Showing 5 changed files with 17 additions and 7 deletions.
diff --git 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
@@ -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
@@ -71,7 +71,6 @@ microhomology
 Mmusculus
 mutect
 Mutect
-MuTect
 NN
 nucleotides
 opar

diff --git a/man/MakeDataFrameFromMutectVCF.Rd b/man/MakeDataFrameFromMutectVCF.Rd
diff --git a/man/ReadMutectVCF.Rd b/man/ReadMutectVCF.Rd