countHumanParalogs: countHumanParalogs

In chapmandu2/CollateralVulnerability2016: Collateral Vulnerability Pipeline

Description

This function uses the biomaRt package to extract paralog information for supplied human genes

Usage

countHumanParalogs(con, genes, alt_mart = NULL)

Arguments

con	A SQLiteConnection object
genes	A vector of ENSEMBL gene ids
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()
all_genes <- getAllHumanGenes(ex_con)
set.seed(20120806)
ex_genes <- sample(all_genes$gene_id, 100)

#count paralogs
ex_df <- countHumanParalogs(ex_con, ex_genes)
ex_df[1:10,1:2]

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

#larger set of genes
countHumanParalogs(ex_con, sample(all_genes$gene_id, 2000))[1:10,1:2]

#Specify which Mart to use
my_mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="sep2015.archive.ensembl.org")
ex_df <- countHumanParalogs(ex_con, ex_genes, alt_mart=my_mart)
ex_df[1:10,1:2]

## End(Not run)

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