gson: construct a 'GSON' object
In gson: Base Class and Methods for 'gson' Format

gson	R Documentation

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
)

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

Value

A 'GSON' instance

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)

gson documentation built on March 7, 2023, 7:47 p.m.