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]