gson (version 0.1.0)

gson: construct a 'GSON' object

Description

construct a 'GSON' object

Usage

gson(
  gsid2gene,
  gsid2name = NULL,
  gene2name = NULL,
  species = NULL,
  gsname = NULL,
  version = NULL,
  accessed_date = NULL,
  keytype = NULL,
  info = NULL
)

Value

A 'GSON' instance

Arguments

gsid2gene

A data frame with first column of gene set IDs and second column of genes

gsid2name

A data frame with first column of gene set IDs and second column of gene set names

gene2name

A data frame with first column of genes and second column of gene symbols

species

Which species of the genes belongs to

gsname

Name of the gene set (e.g., GO, KEGG, etc.)

version

version of the gene set

accessed_date

date to obtain the gene set data

keytype

keytype of genes

info

extra information

Examples

wpfile <- system.file('extdata', "wikipathways-20220310-gmt-Homo_sapiens.gmt", package='gson')
x <- read.gmt.wp(wpfile)
gsid2gene <- data.frame(gsid=x$wpid, gene=x$gene)
gsid2name <- unique(data.frame(gsid=x$wpid, name=x$name))
species <- unique(x$species)
version <- unique(x$version)
gson(gsid2gene=gsid2gene, gsid2name=gsid2name, species=species, version=version)