fromOwn: build Own annotation database with user defined annotation...

In guokai8/bioAnno: Build Annotation From Online Database

build Own annotation database with user defined annotation file

Description

build Own annotation database with user defined annotation file

Usage

fromOwn(
  geneinfo = geneinfo,
  keytype = NULL,
  gene2go = NULL,
  gene2path = NULL,
  gene2symbol = NULL,
  gene2refseq = NULL,
  gene2ensembl = NULL,
  gene2pfam = NULL,
  gene2reactome = NULL,
  gene2ko = NULL,
  gene2interpro = NULL,
  gene2entrezid = NULL,
  gene2biocyc = NULL,
  gene2kd = NULL,
  gene2fundo = NULL,
  gene2gad = NULL,
  version = NULL,
  maintainer = NULL,
  author = NULL,
  outputDir = NULL,
  tax_id = NULL,
  genus = NULL,
  species = NULL,
  install = TRUE,
  pkgname = NULL,
  rebuild = FALSE
)

Arguments

geneinfo	gene information table with two columns as default("GID","DESCRIPTION")
keytype	key type for building the annotation db
gene2go	Gene Onotoly information for genes
gene2path	KEGG Pathway information for genes
gene2symbol	SYMBOL information for genes
gene2refseq	REFSEQ or KO information for genes
gene2ensembl	ENSEMBL or KO information for genes
gene2pfam	PFAM information for genes
gene2reactome	REACTOME Pathway or KO information for genes
gene2ko	KO information for genes
gene2interpro	INTERPRO information for genes
gene2entrezid	ENTREZID information for genes
gene2biocyc	BIOCYC information for genes
gene2kd	KEGG DISEASE information for genes
gene2fundo	FunDO information for genes
gene2gad	GAD information for genes
version	version for the annotation package
maintainer	maintainer for the annotation package
author	author for the annotation package
outputDir	temporary output path
tax_id	taxonomy id for the species
genus	genus for the species
species	species name(common name,kegg.species.code or scientifc name)
install	install the package or not(default: TRUE)
pkgname	package name you want to choose

Value

annotation package

Author(s)

Kai Guo

Examples

## build your own annotation for Arabidopsis thaliana
data(ath)
fromOwn(geneinfo = ath, install = FALSE)

guokai8/bioAnno documentation built on May 8, 2023, 12:42 p.m.