getOrthologs: getOrthologs

In chapmandu2/CollateralVulnerability2016: Collateral Vulnerability Pipeline

Description

This function uses the biomaRt package to get ortholog information for supplied human genes

Usage

getOrthologs(con, genes, species = "mmusculus", alt_mart = NULL)

Arguments

con	A SQLiteConnection object
genes	A vector of ENSEMBL gene ids
species	The ENSEMBL species id eg mmusculus for mouse
alt_mart	A Mart object created using biomaRt::useMart. This should specify hsapiens_gene_ensembl as the dataset.

Value

a data frame

Examples

## Not run: 
ex_con <- setupSQLite()
ex_genes <- c('ENSG00000074800', 'ENSG00000127616')

#get mouse orthologs
getOrthologs(ex_con, ex_genes, species='mmusculus')

#get fly orthologs
getOrthologs(ex_con, ex_genes, species='dmelanogaster')

#view the tables in the database
DBI::dbListTables(ex_con)

#larger set of genes
all_genes <- getAllHumanGenes(ex_con)
set.seed(20120806)
ex_genes2 <- sample(all_genes$gene_id, 2000)
ortho_df <- getOrthologs(ex_con, ex_genes2, species='mmusculus')

#Specify which Mart to use
my_mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="sep2015.archive.ensembl.org")
getOrthologs(ex_con, ex_genes, species='mmusculus', alt_mart=my_mart)
getOrthologs(ex_con, ex_genes, species='dmelanogaster', alt_mart=my_mart)

## End(Not run)

chapmandu2/CollateralVulnerability2016 documentation built on May 13, 2019, 3:27 p.m.