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added keyoutput parameter to setReadable and modified EXTID2NAME func… #66

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added keyoutput parameter to setReadable and modified EXTID2NAME func… #66

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14 changes: 9 additions & 5 deletions R/setReadable.R
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Original file line number Diff line number Diff line change
@@ -1,17 +1,20 @@
##' mapping geneID to gene Symbol
##' mapping geneID to gene Symbol:
##'
##'
##' @title setReadable
##' @param x enrichResult Object
##' @param OrgDb OrgDb
##' @param keyType keyType of gene
##' @param keyType keyType of symbol/gene name
##' @return enrichResult Object
##' @author Yu Guangchuang
##' @export
setReadable <- function(x, OrgDb, keyType="auto") {

# Added keyoutput = 'SYMBOL' as an optional parameter so it accepts other OrgDB columns as output
setReadable <- function(x, OrgDb, keyType="auto", keyoutput = 'SYMBOL') {
OrgDb <- load_OrgDb(OrgDb)
if (!'SYMBOL' %in% columns(OrgDb)) {
warning("Fail to convert input geneID to SYMBOL since no SYMBOL information available in the provided OrgDb...")
if (! keyoutput %in% columns(OrgDb)) {
warning(paste0("Fail to convert input geneID to SYMBOL since no ", keyoutput ," information available in the provided OrgDb..."))
}

if (!(is(x, "enrichResult") || is(x, "groupGOResult") || is(x, "gseaResult") || is(x,"compareClusterResult")))
Expand Down Expand Up @@ -50,7 +53,8 @@ setReadable <- function(x, OrgDb, keyType="auto") {
genes <- x@gene
}

gn <- EXTID2NAME(OrgDb, genes, keyType)
# Added keyoutput as an additional parameter in EXTID2NAME function.
gn <- EXTID2NAME(OrgDb, genes, keyType, keyoutput)


if(isCompare) {
Expand Down
12 changes: 10 additions & 2 deletions R/utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -289,6 +289,7 @@ rebuildAnnoData.internal <- function(eg.do) {
##' @param OrgDb OrgDb
##' @param geneID entrez gene ID
##' @param keytype keytype
##' @param keyoutput keytype
##' @return gene symbol
##' @importMethodsFrom AnnotationDbi select
##' @importMethodsFrom AnnotationDbi keys
Expand All @@ -297,14 +298,21 @@ rebuildAnnoData.internal <- function(eg.do) {
##' @importFrom GOSemSim load_OrgDb
##' @export
##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
EXTID2NAME <- function(OrgDb, geneID, keytype) {
EXTID2NAME <- function(OrgDb, geneID, keytype, keyoutput = "SYMBOL") {
# Added keyoutput = "SYMBOL" as a parameter so it is possible to define other columns as output
my_db <- OrgDb
OrgDb <- load_OrgDb(OrgDb)
kt <- keytypes(OrgDb)
if (! keytype %in% kt) {
stop("keytype is not supported...")
}

if (! keyoutput %in% columns(OrgDb)) {
stop(paste0("keyoutput ", keyoutput ," is not supported in db ", my_db))
}

gn.df <- suppressMessages(select(OrgDb, keys=geneID, keytype=keytype, columns="SYMBOL"))
# I replaced columns="SYMBOL" with columns=keyoutput
gn.df <- suppressMessages(select(OrgDb, keys=geneID, keytype=keytype, columns=keyoutput))
gn.df <- unique(gn.df)
colnames(gn.df) <- c("GeneID", "SYMBOL")

Expand Down