clean hg19 refs

clean hg19 refs to make it truly portable genome
temizna · Sep 11, 2017 · 596cec6 · 596cec6
1 parent 9bbaf15
commit 596cec6
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/mut.to.sigs.input.R b/R/mut.to.sigs.input.R
@@ -67,14 +67,14 @@ mut.to.sigs.input = function(mut.ref, sample.id = 'Sample', chr = 'chr', pos = '
   # If set to default, carry on happily
   if(is.null(bsg)){
     # Remove any entry in chromosomes that do not exist in the BSgenome.Hsapiens.UCSC.hg19::Hsapiens object    
-    unknown.regions <- levels(mut[, chr])[which(!(levels(mut[, chr]) %in% GenomeInfoDb::seqnames(BSgenome.Hsapiens.UCSC.hg19::Hsapiens)))]
+    unknown.regions <- levels(mut[, chr])[which(!(levels(mut[, chr]) %in% GenomeInfoDb::seqnames(bsg)))]
     if (length(unknown.regions) > 0) {
       unknown.regions <- paste(unknown.regions, collapse = ',\ ')
-      warning(paste('Check chr names -- not all match BSgenome.Hsapiens.UCSC.hg19::Hsapiens object:\n', unknown.regions, sep = ' '))      
-      mut <- mut[mut[, chr] %in% GenomeInfoDb::seqnames(BSgenome.Hsapiens.UCSC.hg19::Hsapiens), ]
+      warning(paste('Check chr names -- not all match',bsg,' object:\n', unknown.regions, sep = ' '))      
+      mut <- mut[mut[, chr] %in% GenomeInfoDb::seqnames(bsg), ]
     }
     # Add in context
-    mut$context = BSgenome::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, mut[,chr], mut[,pos]-1, mut[,pos]+1, as.character = T)
+    mut$context = BSgenome::getSeq(bsg, mut[,chr], mut[,pos]-1, mut[,pos]+1, as.character = T)
   }
 
   # If set to another build, use that one