idConvert: idConvert

In abc-igmm/transcripTools: Collection of functions for analysing gene expression data

Description

Provided with a character vector of genomic identifiers; and a biomaRt hsapiens_gene_ensembl specific set of filters and attributes (i.e. the id format of the input and output respectively); this function returns a data frame with the corresponding mappings of the given identifiers to each of specified attributes.

Usage

idConvert(ids, format_in = "ensembl_gene_id", format_out = "hgnc_symbol")

Arguments

ids	A vector of genomic identifiers
format_in	Format/type of genomic identifiers of the ids input
format_out	Format/type of genomic identifiers to be returned

Details

The 'format_in' argument defaults to ensembl gene id, and the mapped 'format_out' argument defaults to hgnc symbol.

Common filters/attributes are "ensembl_gene_id", "hgnc_symbol", "entrezgene", "illumina_humanht_12_v4" and "affy_hg_u133a".

Credit to Gil Tomas for the original code. Requires biomaRt and internet access.

Value

A 2-column dataframe of original and converted ids

Examples

id_vec <- c("ESR1", "ERBB2", "AURKA")

idConvert(ids = id_vec,
                format_in = "hgnc_symbol",
                format_out = "entrezgene"
                )

abc-igmm/transcripTools documentation built on May 20, 2019, 3:05 p.m.