Nothing
read2_paths <-
function (ordered_alldata = "", gs_locs = "", sets_from = "workspace",
sets_prefix = "RHSA", level = "snp",envir= "")
{
print("Arguments set:")
print(paste("Ordered dataset: ", substitute(ordered_alldata),
sep = ""))
print(paste("Gene Annotations: ", substitute(gs_locs)))
print(paste("Gene-sets Location: ", sets_from))
print(paste("Gene-sets prefix: ", sets_prefix))
print(paste("Annotation level: ", level))
if (missing(level) == TRUE) {
stop("Argument \"level\" must be defined. Permutations performed at \"gene\" or \"snp\" level")
}
if (level != "snp"){
if(level != "gene") {
stop("Argument \"level\" must be \"snp\" or \"gene\"")
}
}
if (sets_from != "workspace"){
if(sets_from != "directory") {
stop("Argument \"from\" must be \"workspace\" or \"directory\"")
}
}
if (sets_from == "workspace") {
ps <- ls(pattern = sets_prefix, envir = envir)
if (length(ps) == 0) {
stop("No pathways/gene-sets found in workspace, if data saved at working directory modify the argument \"sets_from\" to \"directory\"")
}
}
if (sets_from == "directory") {
ps <- list.files(pattern = sets_prefix)
if (length(ps) == 0) {
stop("No pathways/gene-sets found in directory, if data saved at workspace modify the argument \"sets_from\" to \"workspace\"")
}
}
ttl_paths <- length(ps)
paths_ids <- list()
paths_names <- NULL
per_ors <- list()
indx_paths <- NULL
per_orids_list <- NULL
pathways <- matrix(data = 0, ncol = 4, nrow = ttl_paths)
for (i in 1:ttl_paths) {
if (sets_from == "workspace") {
moe <- ps[i]
genes <- get(ps[i],envir=envir)
}
if (sets_from == "directory") {
moe <- strsplit(ps[i], split = "[/.]")[[1]][1]
genes <- as.numeric(read.table(ps[i], header = F,
sep = " "))
}
paths_names <- c(paths_names, moe)
per_orids_list <- c(per_orids_list, paste("per_orids_",
moe, sep = ""))
paths_ids <- c(paths_ids, list(moe = genes))
pathways[i, 1] <- moe
ids <- NULL
ids2 <- NULL
pathways[i, 2] <- length(genes)
for (j in 1:length(genes)) {
x <- which(as.numeric(gs_locs[, 4]) == as.numeric(genes[j]))
if (length(x) != 0) {
ids <- c(ids, x)
}
y <- which(as.numeric(as.character(ordered_alldata[,
4])) == as.numeric(genes[j]))
if (length(y) != 0) {
ids2 <- c(ids2, y)
}
if (j == length(genes)) {
pathways[i, 3] <- length(ids)
pathways[i, 4] <- length(ids2)
}
}
if (level == "snp") {
per_ors <- c(per_ors, list(ids2))
}
if (level == "gene") {
per_ors <- c(per_ors, list(ids))
}
}
names(paths_ids) <- paths_names
names(per_ors) <- per_orids_list
colnames(pathways) <- c("ID", "GenesInPath", "GenesFound",
"SNPsInPath")
return(list(pathways = pathways, per_ors = per_ors))
}
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