Added consensus exons option for exonTable

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: crisprDesign
 Title: Comprehensive design of CRISPR gRNAs for nucleases and base editors
-Version: 0.99.176
+Version: 0.99.177
 Authors@R: c(
  person("Jean-Philippe", "Fortin", email = "[email protected]", role = c("aut", "cre")),
  person("Luke", "Hoberecht", email = "[email protected]", role = c("aut"))

R/addExonTable.R

@@ -14,8 +14,11 @@
 #' @param valueColumn String specifying column in
 #' \code{geneAnnotation(guideSet)} to use as values in the 
 #' output exon table. 
+#' @param useConsensusIsoform Should a consensus isoform be used to 
+#' annotate exons? FALSE by default. If TRUE, the isoform constructed
+#' by \code{getConsensusIsoform} will be used. 
 #' 
-#' @return A \linkS4class{GuideSet} object with a "exinTable" DataFrame
+#' @return A \linkS4class{GuideSet} object with a "exonTable" DataFrame
 #' stored in \code{mcols(guideSet)}. The entries in the DataFrame
 #' correspond to the values specified by \code{valueColumn}.
 #' Rows correspond to gRNAs in the GuideSet, columns correspond to 
@@ -43,7 +46,57 @@
 addExonTable <- function(guideSet,
  gene_id,
  txObject,
- valueColumn="percentCDS"
+ valueColumn="percentCDS",
+ useConsensusIsoform=FALSE
+){
+ if (useConsensusIsoform){
+ gs <- addExonTable_consensusIsoform(guideSet=guideSet,
+ gene_id=gene_id,
+ txObject=txObject)
+ } else {
+ gs <- addExonTable_allIsoforms(guideSet=guideSet,
+ gene_id=gene_id,
+ txObject=txObject,
+ valueColumn=valueColumn)
+ }
+ return(gs)
+}
+
+
+
+addExonTable_consensusIsoform <- function(guideSet,
+ gene_id,
+ txObject
+){
+ consensus <- getConsensusIsoform(gene_id=gene_id,
+ txObject=txObject)
+ exonids <- unique(consensus$exon_id)
+ guides <- names(guideSet)
+ out <- matrix(NA,
+ nrow=length(guides),
+ ncol=length(exonids))
+ rownames(out) <- guides
+ colnames(out) <- exonids
+ out <- as.data.frame(out)
+
+ # Looking at overlap:
+ gr <- getCutSiteRanges(guideSet,
+ nuclease=crisprNuclease(guideSet))
+ df <- findOverlaps(gr, consensus, ignore.strand=TRUE)
+ df <- as.data.frame(df)
+ for (k in seq_len(nrow(df))){
+ out[df[k,1],df[k,2]] <- 1
+ } 
+ out <- DataFrame(out)
+ mcols(guideSet)$exonTable <- out
+ return(guideSet)
+}
+
+
+addExonTable_allIsoforms <- function(guideSet,
+ gene_id,
+ txObject,
+ valueColumn="percentCDS"
 ){
  stopifnot(.hasGeneAnnotation(guideSet))
 
@@ -76,3 +129,7 @@ addExonTable <- function(guideSet,
  return(guideSet)
 }
 
+
+
+
+