corrected copy number string fix

Fixes #56 where the corrected_copy_number is accurate but the corrected_call is HLAMP by default - now the corrected_call will show the proper copy state string Also modified setGenomeStyle so that there is an option to not exclude extra chromosomes that are not the major 1:22, X, Y chrs
gavinha · Dec 7, 2018 · c3061ea · c3061ea
1 parent 60408ca
commit c3061ea
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Showing 2 changed files with 13 additions and 7 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -484,16 +484,19 @@ getPositionOverlap <- function(chr, posn, dataVal) {
 	return(hitVal) 
 }
 
-setGenomeStyle <- function(x, genomeStyle = "NCBI", species = "Homo_sapiens"){
+setGenomeStyle <- function(x, genomeStyle = "NCBI", species = "Homo_sapiens", 
+	filterExtraChr = TRUE){
 	#chrs <- genomeStyles(species)[c("NCBI","UCSC")]
 	if (!genomeStyle %in% seqlevelsStyle(as.character(x))){
     	x <- suppressWarnings(mapSeqlevels(as.character(x), 
     					genomeStyle, drop = FALSE)[1,])
     }
 
-    autoSexMChr <- extractSeqlevelsByGroup(species = species, 
-    				style = genomeStyle, group = "all")
-    x <- x[x %in% autoSexMChr]
+    if (filterExtraChr){
+		autoSexMChr <- extractSeqlevelsByGroup(species = species, 
+						style = genomeStyle, group = "all")
+		x <- x[x %in% autoSexMChr]
+	}
     return(x)
 }
 
@@ -1194,9 +1197,9 @@ correctIntegerCN <- function(cn, segs, purity, ploidy, maxCNtoCorrect.autosomes
 
 	# TITAN calls adjusted for >= copies - HLAMP
 	segs[Chromosome %in% chrs & Copy_Number >= maxCNtoCorrect.autosomes, Corrected_Copy_Number := as.integer(round(logR_Copy_Number))]
-	segs[Chromosome %in% chrs & Copy_Number >= maxCNtoCorrect.autosomes, Corrected_Call := "HLAMP"]
+	segs[Chromosome %in% chrs & Copy_Number >= maxCNtoCorrect.autosomes, names[Corrected_Copy_Number + 1]]
 	cn[Chr %in% chrs & CopyNumber >= maxCNtoCorrect.autosomes, Corrected_Copy_Number := as.integer(round(logR_Copy_Number))]
-	cn[Chr %in% chrs & CopyNumber >= maxCNtoCorrect.autosomes, Corrected_Call := "HLAMP"]
+	cn[Chr %in% chrs & CopyNumber >= maxCNtoCorrect.autosomes, names[Corrected_Copy_Number + 1]]
 
 	# TITAN calls adjust for HOMD
 	if (correctHOMD){

diff --git a/man/loadAlleleCounts.Rd b/man/loadAlleleCounts.Rd
@@ -14,7 +14,7 @@
   loadAlleleCounts(inCounts, symmetric = TRUE, 
   		genomeStyle = "NCBI", sep = "\t", header = TRUE)
 
-	setGenomeStyle(x, genomeStyle = "NCBI", species = "Homo_sapiens")
+	setGenomeStyle(x, genomeStyle = "NCBI", species = "Homo_sapiens", filterExtraChr = TRUE)
 }
 
 \arguments{
@@ -39,6 +39,9 @@
   \item{species}{
   	\code{character} denoting the species
   }
+  \item{filterExtraChr}{
+  	\code{logical}; if \code{TRUE}, then will return the list of chromosomes given by \code{extractSeqlevelsByGroup} for the \code{species} and for autosomes and sex chromosomes, which means that only the major chromosomes are returned (i.e. 1:22, X, Y). 
+  }
 }
 
 \value{