# Wrapper function to run CAMERA on different contrasts
runcamera <- function(voom.results, contrast, gs.annot,
num.workers=4, verbose = TRUE){
# run CAMERA and write out ranked 'gene sets' for each 'contrast'
if (is.matrix(contrast)){
contr.names = colnames(contrast)
contr.num = ncol(contrast)
}else{
contr.names = names(contrast)
contr.num = length(contrast)
}
# camera.results = vector("list", ncol(contrast))
args.all = list()
for(i in 1:contr.num){
if (is.matrix(contrast))
args.all[[i]] = list(voom.results = voom.results,
contrast.name = contr.names[i],
contrast = contrast[,i],
gs.annot = gs.annot,
verbose = verbose
)
else
args.all[[i]] = list(voom.results = voom.results,
contrast.name = contr.names[i],
contrast = contrast[i],
gs.annot = gs.annot,
verbose = verbose
)
# print(args.all[[i]])
}
names(args.all) = contr.names
if (Sys.info()['sysname'] == "Windows" || contr.num <= 1)
camera.results = lapply(args.all, runcamera.contrast)
else
camera.results = mclapply(args.all, runcamera.contrast,
mc.cores=num.workers)
# names(camera.results) = colnames(contrast)
return(camera.results)
}
runcamera.contrast <- function(args){
if (args$verbose)
message(" Running CAMERA for ", args$contrast.name)
else
message(".", appendLF = FALSE)
camera.results = camera(y=args$voom.results,
index=args$gs.annot@idx,
design=args$voom.results$design,
contrast=args$contrast) # , allow.neg.cor=TRUE, inter.gene.cor=NA
# print(head(camera.results[[i]]))
camera.results =
camera.results[order(camera.results[,"PValue"]),]
camera.results = cbind(Rank=seq(1,
nrow(camera.results)), camera.results)
colnames(camera.results)[which(colnames(camera.results) == "PValue")] = "p.value"
colnames(camera.results)[which(colnames(camera.results) == "FDR")] = "p.adj"
return(camera.results)
}
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