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##copyright 2004 R. Gentleman, all rights reserved
##given the name of chip compute the pathway adjacency matrix for LLids
PWAmat = function(data) {
if(!is.character(data) || length(data) != 1 )
stop("wrong argument")
if( length(grep("^org\\..+\\.sgd$", data))>=1 ){
dataE = getAnnMap("PATH2ORF", data, load=TRUE, type="db")
}
else if ( length(grep("^org\\..+\\.eg$", data))>=1 ){
dataE = getAnnMap("PATH2EG", data, load=TRUE, type="db")
}
else {
dataE = getAnnMap("PATH2PROBE", data, load=TRUE, type=c("db"))
}
if( data == "YEAST" || length(grep("^org\\..+", data))>=1 )
pathLL = as.list(dataE)
else {
pathLL = eapply(dataE, function(x) {
x = x[!is.na(x)]
if(length(x)>0){
LLs = getEG(x, data)
LLs = LLs[!is.na(LLs)]
unique(LLs) }
})
}
uniqLL = unique(unlist(pathLL,use.names=FALSE))
Amat = sapply(pathLL, function(x) {
mtch = match(x, uniqLL)
zeros = rep(0, length(uniqLL))
zeros[mtch] = 1
zeros})
dimnames(Amat) = list(uniqLL, names(pathLL))
return(Amat)
}
##given the name of chip compute the PubMed adjacency matrix for probe set ids
PMIDAmat = function(pkg, gene=NULL) {
if(!is.character(pkg) || length(pkg) != 1 )
stop("wrong argument")
probe2pmid <- get(paste(pkg, "PMID", sep=""))
if(is.null(gene)){
gene2pmid <- as.list(probe2pmid)
}else{
if(any(duplicated(gene))) warning("Gene is not unique.")
gene2pmid <- mget(unique(gene), probe2pmid, ifnotfound=NA)
}
pmid <- unique(unlist(gene2pmid))
Amat <- sapply(gene2pmid,
function(x){
mtch <- match(x, pmid)
zeros <- rep(0, length(pmid))
zeros[mtch] <- 1
return(zeros)
}
)
dimnames(Amat) = list(pmid, names(gene2pmid))
return(Amat)
}
##given a GO term, and an exprset, produce a heatmap of all probes
##mapped to that GOterm;
GO2heatmap = function(x, eset, data, ...) {
if( missing(data) )
data = annotation(eset)
mapE = get(paste(data, "GO2ALLPROBES", sep=""))
whG = mapE[[x]]
##need this because there could be multiple criteria
whG = unique(whG)
whGs = whG[whG %in% featureNames(eset)]
dataM = exprs(eset)[whGs,]
heatmap(dataM, ...)
}
GOmnplot = function (x, eset, data = "hgu133plus2", group, ...)
{
mapE = get(paste(data, "GO2ALLPROBES", sep = ""))
whG = mapE[[x]]
whG = unique(whG)
whGs = whG[whG %in% featureNames(eset)]
dataM = exprs(eset)[whGs, ]
tts = apply(dataM, 1, function(x) sapply(split(x, group), mean))
rn = row.names(tts)
if( length(levels(factor(group))) != 2 )
stop("only works for factors with two levels")
plot(tts[1,], tts[2,], xlab=rn[1], ylab=rn[2], ...)
abline(a=0, b=1)
return(tts)
}
p2LL = function(data) {
.Defunct("p2LL", package="annotate")
}
setGeneric("KEGG2heatmap", function(x, eset, data, ...)
standardGeneric("KEGG2heatmap"))
setMethod("KEGG2heatmap", c("character", "eSet", "character"),
function(x, eset, data, ...) {
if( missing(data) )
data = annotation(eset)
mapE = get(paste(data, "PATH2PROBE", sep = ""))
whG = mapE[[x]]
whG = unique(whG)
whGs = whG[whG %in% featureNames(eset)]
dataM = exprs(eset)[whGs, ]
heatmap(dataM, ...)
})
setMethod("KEGG2heatmap", c("character", "matrix", "character"),
function(x, eset, data, ...) {
mapE = get(paste(data, "PATH2PROBE", sep = ""))
whG = mapE[[x]]
whG = unique(whG)
whGs = whG[whG %in% row.names(eset)]
dataM = eset[whGs, ]
heatmap(dataM, ...)
})
setGeneric("KEGGmnplot", function(x, eset, data= "hgu133plus2", group,
...) standardGeneric("KEGGmnplot"))
setMethod("KEGGmnplot", c("character", "eSet", "character"),
function (x, eset, data = "hgu133plus2", group, ...) {
mapE = get(paste(data, "PATH2PROBE", sep = ""))
whG = mapE[[x]]
whG = unique(whG)
whGs = whG[whG %in% featureNames(eset)]
dataM = exprs(eset)[whGs, ]
tts = apply(dataM, 1, function(x) sapply(split(x, group), mean))
rn = row.names(tts)
if( length(levels(factor(group))) != 2 )
stop("only works for factors with two levels")
plot(tts[1,], tts[2,], xlab=rn[1], ylab=rn[2], ...)
abline(a=0, b=1)
return(tts)
})
setMethod("KEGGmnplot", c("character", "matrix", "character"),
function (x, eset, data = "hgu133plus2", group, ...) {
mapE = get(paste(data, "PATH2PROBE", sep = ""))
whG = mapE[[x]]
whG = unique(whG)
whGs = whG[whG %in% row.names(eset)]
dataM = eset[whGs, ]
tts = apply(dataM, 1, function(x) sapply(split(x, group), mean))
rn = row.names(tts)
if( length(levels(factor(group))) != 2 )
stop("only works for factors with two levels")
plot(tts[1,], tts[2,], xlab=rn[1], ylab=rn[2], ...)
abline(a=0, b=1)
return(tts)
})
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