Slight changes to output file format

imgag · Sep 12, 2018 · 9dbeb58 · 9dbeb58
1 parent f0e0d6b
commit 9dbeb58
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/somatic/firstStep.R b/somatic/firstStep.R
@@ -523,8 +523,9 @@ for (sam_no in 1:ncol(matrixOfLogFold)) {
   }
   fileToOut <- paste0(folder_name, sample_name, "/CNAs.txt")
   fileConn<-file(fileToOut)
-  writeLines(c(paste("##"," QC ", finalPValue, collapse = " ")), fileConn)
+  writeLines(c(paste("##"," QC ", signif(finalPValue,2), collapse = " ")), fileConn)
   close(fileConn)
+  print(found_CNVs_total)
   write.table(found_CNVs_total, file = fileToOut, quote=F, row.names = F, sep="\t", append = T)	
   }  
 }
diff --git a/somatic/helpersSomatic.R b/somatic/helpersSomatic.R
@@ -83,7 +83,7 @@ plotFoundCNVs <- function(found_CNVs, toyLogFoldChange, toyBedFile, outputFolder
       if(opt$debug) {
         print(annotationGenes)
       }
-      CNVtoOut <- matrix(c(chrom, toyBedFile[found_CNVs[s,2],2], toyBedFile[found_CNVs[s,3],3], vector_of_states[found_CNVs[s,4]], -1 * found_CNVs[s,1], annotationGenes), nrow=1)
+      CNVtoOut <- matrix(c(chrom, toyBedFile[found_CNVs[s,2],2], toyBedFile[found_CNVs[s,3],3], vector_of_states[found_CNVs[s,4]], round(-1 * found_CNVs[s,1],0), annotationGenes), nrow=1)
       if(opt$debug)
       {
         print(CNVtoOut)