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findNeighbors <- function(chrLoc, llID, chromosome, upBase, downBase,
mergeOrNot = TRUE){
require(chrLoc, character.only = TRUE) ||
stop(paste("Chromomosome location chrLoc",
"is not available on the system",
"Either build one or get one from",
"BioConductor"))
if(checkArgs(llID, chromosome, upBase, downBase) == "swap"){
temp <- upBase
upBase <- downBase
downBase <- temp
}
upBase <- as.numeric(ifelse(missing(upBase), 0, upBase))
downBase <- as.numeric(ifelse(missing(downBase), 0, downBase))
if(missing(chromosome)){
chromosome <- findChr4LL(llID, get(paste(chrLoc,
"LOCUSID2CHR", sep = "")),
gsub("CHRLOC", "", chrLoc))
}
if(!missing(llID)){
# Find the location for the target gene
location <- as.numeric(get(llID, get(paste(chrLoc,
chromosome, "START", sep = ""))))
}else{
location <- (downBase - upBase)/2
}
upperB <- getBoundary(location, upBase, TRUE)
downB <- getBoundary(location, downBase, FALSE)
neighbors <- list()
# There may be chances that a llID be mapped to genes on different CHR
for(i in chromosome){
start <- unlist(contents(get(paste(chrLoc, chromosome,
"START", sep=""))),
use.names=TRUE)
end <- unlist(contents(get(paste(chrLoc, chromosome,
"END", sep=""))),
use.names=TRUE)
if(!missing(llID)){
# greb the ones in the range
foundUp <- weightByConfi(start[start > upperB &
start < min(location)])
foundDown <- weightByConfi(end[end < downB &
end > max(location)])
if(length(foundUp) != 0 || length(foundDown) != 0){
if(mergeOrNot){
neighbors[[as.character(i)]] <- unique(c(foundUp,
foundDown))
}else{
neighbors[[as.character(i)]] <-
list(upstream = foundUp, downstream = foundDown)
}
}
}else{
found <- weightByConfi(c(start[start >= upperB &
start <= location],
end[end <= downB & end >= location]))
if(length(found) != 0){
neighbors[[as.character(i)]] <- unique(found)
}
}
}
if(length(neighbors) == 0){
warning("No Genes in the defined region satisfy the condition")
}else{
return(neighbors)
}
}
checkArgs <- function(llID, chromosome, upBase, downBase){
# llID is not required if search for genes within a range
if(missing(llID)){
# Both upBase, downBase, and chromosome must be there if
# llID is missing
if(any(missing(upBase), missing(downBase), missing(chromosome))){
stop(paste("Search can not be conducted with llID and",
"at least one of upBase, downBase and ",
"chromosome missing"))
}else{
if(as.numeric(upBase) < as.numeric(downBase)){
warning(paste("upBase value is smaller then downBase",
"value. Values have been swapped"))
return("swap")
}
if(as.numeric(upBase) == as.numeric(downBase)){
stop("upBase and downBase can not be the same")
}
}
}else{
if(missing(upBase)){
warning(paste("upBase is missing. Search will be",
"conducted for genes downstream only"))
}
if(missing(downBase)){
warning(paste("downBase is missing. Search will be",
"conducted for genes upstream only"))
}
}
return("OK")
}
findChr4LL <- function(llID, chrEnv, organism){
options(show.error.message = FALSE)
chr <- try(chrEnv[[llID]])
options(show.error.message = TRUE)
if(inherits(chr, "try-error")){
stop(paste("Entrez Gene ID", llID, "could not be found in any",
"of the chromosomes in the data package"))
}else{
if(length(chr) == 1){
if(!is.element(chr, getValidChr(organism))){
warning(paste("Entrez Gene ID", llID, "is currently",
"not known to be associated with any",
"chromosome"))
}
return(chr)
}else{
chr <- chr[is.element(chr, getValidChr(organism))]
return(unique(chr))
}
}
}
getValidChr <- function(organism){
switch(toupper(organism),
HUMAN = return(c(1:22, "X", "Y")),
MOUSE = return(c(1:19, "X", "Y")),
RAT = return(c(1:20, "X", "Y")),
stop(paste("Unknow organism", organism)))
}
getBoundary <- function(loc, base, lower = TRUE){
if(as.numeric(loc[1]) == 0){
return(base)
}else{
if(lower){
boundary <- as.numeric(loc[1]) - base
if(boundary < 0){
return(0)
}else{
return(boundary)
}
}else{
return(as.numeric(loc[1]) + base)
}
}
}
weightByConfi <- function(foundLLs){
if(length(foundLLs) != 0){
temp <- unique(names(foundLLs))
foundLLs <- gsub("(^.*)\\..*", "\\1", temp)
names(foundLLs) <- gsub("^.*\\.(.*)", "\\1", temp)
# Remove LLs named Unconfident if one named Confident exists
if(any(duplicated(foundLLs))){
foundLLs <- c(foundLLs[names(foundLLs) == "Confident"],
foundLLs[names(foundLLs) != "Confident"])
foundLLs <- foundLLs[!duplicated(foundLLs)]
}
return(foundLLs)
}else{
return("")
}
}
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