getGeneInfo: Get gene information

Description Usage Arguments Value Examples

View source: R/VCF_Utils.R

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

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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

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

wrightrc/r1001genomes documentation built on Nov. 20, 2018, 1:22 a.m.