geneAnno: annotate gene name or map for entrez id or symbol

In jmzeng1314/humanid: gene id annotation

Description

So far, we accept entrez gene id or symbol as input to be annotated. such as 7157 or TP53. you just need to assign the geneLists,a character vector Then we'll annotate the name by default, and also you can choose map,ensembl,accnum to be annotated or not. lastly, you can output the annotation to a html file,just like:geneAnno(kegg2GeneID[['01212']],file = T,prefix = as.character(kegg2name['01212','pathway_name']) for each kegg pathway, you will like this function I guess. So have a fun .

Usage

geneAnno(geneLists = c(1, 2, 9), name = T, map = F, ensembl = F,
  accnum = F, file = F, prefix = "test")

Arguments

geneLists	a character vector for gene entrez ID list,default: c(1,2,9)
name	choose whether annotate gene name for the gene id or not , default : T
map	choose whether annotate gene map for the gene id or not , default : F
ensembl	choose whether annotate gene ensembl for the gene id or not , default : F
accnum	choose whether annotate gene accnum for the gene id or not , default : F
file	choose whether print the annotate results into a file or not , default : F
prefix	define the prefix for the output file, default : test

Value

a data.frame which has more than 2 column

Examples

geneAnno();geneAnno('TP53');geneAnno(kegg2GeneID[['01212']],file = T,prefix = as.character(kegg2name['01212','pathway_name'])
lapply(names(kegg2GeneID),function(x) geneAnno(kegg2GeneID[[x]],file = T,prefix = as.character(kegg2name[x,'pathway_name'])))

jmzeng1314/humanid documentation built on May 19, 2019, 2:57 p.m.