retrieveOrthologs {RCAS}R Documentation

retrieveOrthologs

Description

Given two biomart connections and a set of entrez gene identifiers; retrieve orthologs between mart1 and mart2 for the given list of genes

Usage

retrieveOrthologs(mart1, mart2, geneSet)

Arguments

mart1

An Ensembl biomart connection for reference species created using the biomaRt::useMart() function

mart2

An Ensembl biomart connection for target species created using the biomaRt::useMart() function

geneSet

A vector of Entrez gene ids from a reference species (should be available at the biomart object, mart1)

Value

A data.frame object containing a mapping of orthologouse genes from two mart objects

Examples

mart1_hg19 <- biomaRt::useMart(biomart = 'ENSEMBL_MART_ENSEMBL',
                                  host = 'feb2014.archive.ensembl.org',
                               dataset = "hsapiens_gene_ensembl")
mart2_mm9 <- biomaRt::useMart(biomart = 'ENSEMBL_MART_ENSEMBL',
                                 host = 'may2012.archive.ensembl.org',
                              dataset = "mmusculus_gene_ensembl")
genes <- c('2645','5232', '5230','5162','5160')
orthologs <- retrieveOrthologs( mart1 = mart1_hg19,
                                mart2 = mart2_mm9,
                                geneSet = genes)

[Package RCAS version 1.6.0 Index]