unionRefTr: Union introns/exons of transcripts

In IntEREst: Intron-Exon Retention Estimator

Description

Performs union on the overlapping introns/exons so that the final merged transcripts would feature from each exon or intron, one copy.

Usage

unionRefTr( referenceChr, referenceBegin, referenceEnd, referenceTr, 
	referenceIntronExon, intronExon="exon", silent=FALSE)

Arguments

referenceChr	Chromosome names of the references (e.g. introns).
referenceBegin	A vector that corresponds to the begin coordinates of the reference.
referenceEnd	A vector that corresponds to the end coordinates of the reference.
referenceTr	A character vector that includes transcription IDs.
referenceIntronExon	A vector with the same size as the referenceChr, referenceBegin and referenceEnd which contains 'intron' and 'exon' describing what (either intron or exon) each element of the 3 vectors represents.
intronExon	Should be assigned either 'intron' or 'exon' or c('intron','exon') based on whether match the PWM to the intronic, exonic, or intronic and exonic regions of the reference. By default it seeks matches in intronic regions (intronExon='intron').
silent	Whether run silently.

Value

Data frame containing merged transcripts structure. The merged transcripts feature from each intron or exon, one copy ONLY.

Author(s)

Ali Oghabian

See Also

annotateU12.

Examples

unU12Ex<-unionRefTr( referenceChr=u12[1:94,"chr"], 
	referenceBegin=u12[1:94,"begin"], referenceEnd=u12[1:94,"end"], 
	referenceTr=u12[1:94,"trans_name"], 
	referenceIntronExon=u12[1:94,"int_ex"], intronExon="exon", silent=TRUE)

unU12Int<-unionRefTr( referenceChr=u12[1:94,"chr"], 
	referenceBegin=u12[1:94,"begin"], referenceEnd=u12[1:94,"end"], 
	referenceTr=u12[1:94,"trans_name"], 
	referenceIntronExon=u12[1:94,"int_ex"], intronExon="intron", silent=TRUE)

unU12IntEx<-unionRefTr( referenceChr=u12[1:94,"chr"], 
	referenceBegin=u12[1:94,"begin"], referenceEnd=u12[1:94,"end"], 
	referenceTr=u12[1:94,"trans_name"], 
	referenceIntronExon=u12[1:94,"int_ex"], intronExon=c("intron","exon"), 
	silent=TRUE)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.