geneRegionBiomart: Construct an AnnotationTrack object from biomaRt.

Description Usage Arguments Value Author(s)

View source: R/GenomeGraphs-classes.R

Description

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

Usage

1
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


GenomeGraphs documentation built on May 20, 2017, 10:02 p.m.

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