Merge branch 'master' into development

AG-Boerries · Oct 26, 2020 · cee3583 · cee3583
2 parents 962748c + 8efea58
commit cee3583
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Showing 3 changed files with 4 additions and 5 deletions.
diff --git a/RScripts/Main.R b/RScripts/Main.R
@@ -368,7 +368,6 @@ if (protocol == "tumorOnly"){
 print("Mutation Signature Analysis.")
 if( protocol == "somaticGermline" | protocol == "somatic"){
   somaticVCF <- paste0(path_input, sample,"_vc.output.snp.Somatic.hc.fpfilter.vcf")
-  targetCapture_cor_factors <- paste(path_data, "targetCapture_cor_factors.rda", sep = "/")
   mut_sig_ana <- mut_sig_wCI(vcf_file = somaticVCF, cutoff = 0.01, sample = sample, sureselect_type = sureselect_type, path_script = path_script, ref_genome = ref_genome, targetCapture_cor_factors, path_output = path_output)
 } else {
   vcf <- paste0(path_input, sample,"_vc.output.snp.fpfilter.vcf")

diff --git a/RScripts/Report.Rnw b/RScripts/Report.Rnw
@@ -249,8 +249,8 @@ if(dim(mutation_analysis_result$table_loh_mutations)[1] != 0) {
     tmp$condel.label[which(is.na(tmp$condel.label))] <- "."
     tmp$AAChange <- gsub(pattern = ";", replacement = "; ", x = tmp$AAChange)
     tmp <- tmp[order(tmp$VAF_Tumor, decreasing =  TRUE), , drop = FALSE]
-    tmp <- tmp[, c(19, 2, 4, 3, 21:20, 12:13, 22, 10:9)]
-    #tmp <- tmp[, c(1:2, 4, 3, 6, 5, 10:11, 15, 14, 13)]
+    #tmp <- tmp[, c(19, 2, 4, 3, 21:20, 12:13, 22, 10:9)]
+    tmp <- tmp[, c(1:2, 4, 3, 6, 5, 10:11, 15, 14, 13)]
     colnames(tmp) <- c("Gen", "Genname", "AA-Austausch", "Funktion", "VAF (Coverage) Tumor", "VAF (Coverage) Keimbahn", "MAF", "Condel", "Cosmic", "OG", "TSG")
     kable(tmp, format = "latex", caption = "Identifizierte Loss of Heterozygosity geordnet nach VAF in der Tumorprobe \\label{loh_cg}", booktabs = T, longtable = T, digits = 2, row.names = F, escape = FALSE) %>% kable_styling(latex_options = c( "HOLD_position", "repeat_header"), font_size = 9) %>% column_spec(c(2, 9), width = "6em") %>% column_spec(c(1, 3), width = "5em") %>% column_spec(c(4:6), width = "3em") %>% column_spec(c(8, 10:11), width = "2em") %>% row_spec(0, angle = 60)
   } else {

diff --git a/RScripts/filtering_tools.R b/RScripts/filtering_tools.R
@@ -1216,7 +1216,7 @@ txt2maf <- function(input, Center = center, refBuild = 'GRCh37', idCol = NULL, i
                                     Score = "",
                                     BAM_File = "",
                                     Sequencer = "",
-                                    HGSVp_Short = proteinChange,
+                                    HGVSp_Short = proteinChange,
                                     Amino_Acid_Change = proteinChange,
                                     TxChange = TxChange,
                                     Transcript_Id = Transcript_Id,
@@ -1246,4 +1246,4 @@ exclude <- function(x, vaf = 5){
     x <- x[id, ]
   }
   return(x)
-}
+}