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ZG-comments-for-Gmt2GeneCat.R #3

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14 changes: 9 additions & 5 deletions R/Gmt2GeneCat.R
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Original file line number Diff line number Diff line change
@@ -1,13 +1,17 @@
#' Gmt2GeneCat
#'
#' Read a gmt file, and return a list with its name
#' being a gene id based on gene_anno_file, and each element of this list
#' being the pathways that this gene corresponds to
#' being a gene id based on gene_anno_file, and each element of this list
#' being the pathways that this gene corresponds to#' being the pathways that this gene corresponds to
####ZG
#' Read a gmt file, and return a list named by gene id from gene_anno_file,
#' and each element of this list is the pathways that this gene corresponds to
####ZG
#'
#' @param gmt_input_file input file
#' @param gmt_input_file input file #### input file for somethings
#' @param file.type local or url
#' @param gene_anno_file annotation file
#' @param gene_anno gene annotation to be used if no annotation file
#' @param gene_anno gene annotation #### data or variable #### to be used if no annotation file #### is provided
#'
#' @return a list with its names being geneID, its element being the pathways
#'
Expand Down Expand Up @@ -105,4 +109,4 @@ gene2cat2 <- function(gmt_input_file, file.type) {
names(gene.2.cat) <- gene.name
gene.2.cat

}
}