geneRegionBiomart {GenomeGraphs}R Documentation

Construct an AnnotationTrack object from biomaRt.

Description

This function constructs an AnnotationTrack object from Biomart. It is a convenience function.

Usage

geneRegionBiomart(chr, start, end, strand, biomart, dp = NULL, chrFunction = function(x) x, strandFunction = function(x) x)

Arguments

chr chr An integer
start start The start location
end end The end location
strand strand An integer -1, 0, 1
biomart biomart A mart
dp dp DisplayPars object
chrFunction chrFunction A function which takes chr and converts it into the correct representation for biomaRt. For instance yeast likes to have chromosomes as roman numerals so you can use as.roman here.
strandFunction strandFunction Analagous to chrFunction, but for strand. The internal representation of strand is -1,0,1 whereas biomaRt has different species dependent representations.

Value

An AnnotationTrack object.

Author(s)

James Bullard


[Package GenomeGraphs version 1.2.3 Index]