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 1.14.0
Index]