#' Returns the list of DE genes in a set of pathways
#'
#' @param deIDs a list of differentially expressed genes
#' @param pathwayIDs a list KEGG IDs of pathways for which we want the DEGs
#'
#' @importFrom magrittr %>%
#' @importFrom KEGGgraph translateGeneID2KEGGID
#' @importFrom KEGGgraph translateKEGGID2GeneID
#' @importFrom graph nodes
#'
#' @export
#'
#'
geneReport <- function(deIDs, pathwayList = NULL){
if(is.null(pathwayList)) {
stop("No Pathway List provided")
}else{
tryCatch({
pathList <- paste0(pathwayList,".xml")
a <- CADIA::pathways.collection[pathList]
deKIDs <- KEGGgraph::translateGeneID2KEGGID(deIDs)
genes <- sapply(a, function(X){
isDiffExp <- nodes(X) %in% deKIDs
isDiffExp <- nodes(X)[isDiffExp]
x <- KEGGgraph::translateKEGGID2GeneID(isDiffExp)
q <- stringi::stri_join_list(list(x), sep = "/",
collapse = NULL)
return(q)
})
path.names <- CADIA::pathways.collection.names[pathList]
return(data.frame(path.names,genes))
}, error = function(e){
stop("The pathway list may contain invalid IDs or pathways without
differentially expressed nodes")})
}
}
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