getGeneInfo: Get gene information

In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset

Description

Get the start and end position of each transcript of a set of genes using 'bioMart' package to query the TAIR10 database via plants.ensembl.org

Usage

getGeneInfo(genes, firstOnly = TRUE, useCache = TRUE,
  source = "tair10", verbose = FALSE)

Arguments

genes	a character vector of tair IDs of the genes to retrieve
firstOnly	logical, if true only return transcript IDs containing ".1"
useCache	logical, read from and write to a file of cached genes?
source	the source to retrieve gene information from. "tair10" will use the tair 10 database via biomart (requires internet), "araport11" uses a gff file of the araport11 data stored locally in the r1001genomes R package a file path to a .gff or .gff.gz file may also be used.
verbose	TRUE or FALSE, print new genes added to cache in console?

Value

a table containing fields from the TAIR database on the provided genes including "transcript_ID" and "regionString" columns required for other fuctions in this code

Examples

geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))

wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.