GeneRegionScan (version 1.28.0)

exonStructure: Add exon-structure to plots

Description

Function that will paint the exon structure of a gene on the plots obtained by plotOnGene.

Usage

exonStructure(mrna, genome, maxMismatch=4, y=0)

Arguments

mrna

A gene sequence formatted as DNAstring, DNAstringSet or character-vectors with sequence.

genome

A number of gene sequences as DNAstring, vectors of DNAStrings, DNAstringSet or character-vectors with sequence.

maxMismatch

Integer. The maximum number of mismatches per exon that can be allowed before the exon is not allocated at the position in the template mrna. Defaults to 4.

y

Numeric. The vertical position of the exon structure (if ylim is changed)

Value

• No value, but plots the layout of exons in a gene on the product of a call to plotOnGene.

Details

When given a sequence of the DNA divided by exons and a sequence of the corresponding mRNA string, this function will plot the layout of exons along the length of the x-axis on the current device. The sequences can be given as character vectors with sequence or as DNAString reads using the Biostrings package. Furthermore the genome must be divided with an entry for each exon. This is easily done by downloading the genome sequences of the gene-of-interest from http://genome.ucsc.edu and specifying "One FASTA record per region".

The function works by sequentially comparing each exon to the mrna. The location of the match start and end is taken as the exon boundaries and plotted. If more than one match is found a warning is given. If no match is found for an exon this is printed, but otherwise ignored. The mrna can in fact also be DNA sequence with introns. The important thing is that it serves as template for the exon matching.

Importantly, the exon-numbers technically refer to "number of exon in investigated transcript". For example if an DNA with exon structure for an isoform which does not include all exons in the gene is investigated, then there will be skips of exon numbers. To avoid this, the DNA for an isoform which do include all exons could be used. However, it is really more a biological issue: different sources can differ on where to start the counting for a given gene in any case.

See Also

geneRegionScan, plotOnGene

Examples

data(exampleProbeLevelSet)
	plotOnGene(exampleProbeLevelSet, mrna, label="gender", testType="wilcoxon")
	exonStructure(mrna, genomic, maxMismatch=2)