unionRefTr {IntEREst} | R Documentation

## Union introns/exons of transcripts

### 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)

[Package IntEREst version 1.4.1 Index]