unifyRanges: Unification of Exonic ranges.

In refGenome: Gene and Splice Site Annotation Using Annotation Data from 'Ensembl' and 'UCSC' Genome Browsers

Description

Unified ranges are intended to be used as preparation of exonic coordinates for counting of alignments (reads) inside these regions. In order to prevent ambiguities, overlaps between exons are removed.

Usage

unifyRanges(object)

Arguments

object

refExons object. Contains exonic coordinates data.

Details

Removal of overlaps works as follows: Ranges are sorted according to their seqid and begin value. Ranges which are contained in a precedent range are removed. For ranges with partial overlap with a precedent range, the start position is shifted to one position after the end of the precedent range. The size of the shift is contained in the 'ubs' value. An overview over the size and the number (begin-) shifts can be obtained using the plotUbs function.

Value

The unifyRanges function returns a refExons object. The data table contains the following columns:

id	Numeric index retained from the incoming refExons object.
seqid	Chromosome identifier
begin	begin of range
end	end of range
strand	strand for exon (+ or -)
gene_id	Fene identifier
transcript_id	Transcript identifier
gene_name	Gene name
exon_number	Exon numbe
ubs	Unification begin shift. Number by which begin has been increased during the unification process

Author(s)

Wolfgang Kaisers

Examples

##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ensfile <- system.file("extdata",
                        "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)
enex <- refExons(ens)

saveGenome(enex,"enex.RData", useBasedir=FALSE)
er <- loadGenome("enex.RData")

# Unify exons
uex <- unifyRanges(enex)
plotUbs(uex, xlim=c(0,400), ylim=c(0,5))

##-------------------------------------##
## B) UCSC
##-------------------------------------##
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
ucex <- refExons(uc)
# Unify exons
uex <- unifyRanges(enex)
plotUbs(uex, xlim=c(0,400), ylim=c(0,5))

refGenome documentation built on May 23, 2019, 1:03 a.m.