convertID: convert gene IDs by id map

In GeneNetworkBuilder: GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Description

For same gene, there are multple gene alias. In order to eliminate the possibility of missing any connections, convert the gene symbols to unique gene ids is important. This function can convert the gene symbols to unique ids and convert it back according a giving map.

Usage

convertID(x, IDsMap, ByName = c("from", "to"))

Arguments

x	a matrix or dataframe contain the columns to be converted.
IDsMap	a character vector of the identifier map
ByName	the column names to be converted

Value

a matrix or dataframe with converted gene IDs

Examples

data("ce.IDsMap")
bind<-cbind(from="daf-16", to=c("fkh-7", "hlh-13", "mxl-3", "nhr-3", "lfi-1"))
convertID(toupper(bind), ce.IDsMap, ByName=c("from", "to"))

Example output

Loading required package: Rcpp
     from             to              
[1,] "WBGene00000912" "WBGene00001439"
[2,] "WBGene00000912" "WBGene00001957"
[3,] "WBGene00000912" "WBGene00003511"
[4,] "WBGene00000912" "WBGene00003602"
[5,] "WBGene00000912" "WBGene00022500"

GeneNetworkBuilder documentation built on Nov. 8, 2020, 8:24 p.m.