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LL2homology <- function(homoPkg, llids){
warning("This function has been DEPRECATED.")
if(!require(homoPkg, character.only = TRUE))
stop("Package homology not available!")
hgids <- mget(as.character(llids), envir = get(paste(homoPkg,
"LL2HGID", sep = "")), ifnotfound = NA)
#if(length(hgids) == 1){
# return(HGID2homology(hgids[[1]]))
#}
return(sapply(hgids, HGID2homology, homoPkg = homoPkg))
}
ACC2homology <- function(accs, homoPkg){
warning("This function has been DEPRECATED.")
if(!require(homoPkg, character.only = TRUE))
stop(paste("Package", homoPkg, "not available!"))
hgids <- mget(as.character(accs), envir = get(paste(homoPkg, "ACC2HGID",
sep = ""), pos = match(paste("package:", homoPkg, sep = ""),
search())), ifnotfound = NA)
return(sapply(hgids, HGID2homology, homoPkg))
}
HGID2homology <- function(hgid, homoPkg){
warning("This function has been DEPRECATED.")
homoGenes <- list()
# hgid may be of length greater than 1 as a LL id may be mapped to
# more than 2 HGIDs
for(i in hgid){
options(show.error.messages = FALSE)
tryMe <- try(get(as.character(i),
envir = get(paste(homoPkg, "DATA", sep = ""),
pos = match(paste("package:", homoPkg, sep = ""),
search()))))
options(show.error.messages = TRUE)
if(!inherits(tryMe, "try-error")){
homoGenes[[length(homoGenes) + 1]] <- tryMe
}
}
return(homoGenes)
}
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