R: Unification of splice-junctions.

unifyJuncs {refGenome} | R Documentation

## Unification of splice-junctions.

### Description

Overlaps query ranges with reference ranges. The function assumes that there is no overlap between reference ranges.

### Usage

    unifyJuncs(object)

### Arguments

`object` | `refJunctions` object. Contains splice-junction data.

### Details

Many splices sites are multiple times contained when calculated from transcripts. In order to obtain unique splice positions the function extracts one data set per (seqid, lend, rstart) combination. For each site the annotation information (gene_id, strand, fexid) is extracted from the most abundand gene name. `cnNmd` suffices: 0 <= cnNmd <= nSites. When cnNmd=0, the junction is only present in Transcripts with biotype `nonsense mediated decay`.

### Value

The returned object has the same class as the passed argument (refJunctions or derived). Therefore, it's possible to use unified junctions in the same way in downstream analysis as un-unified junctions. The contained gtf - data.frame contains the following columns:

id | Numeric index for unique site.
seqid | Chromosome identifier
lstart | left start
lend | left end
rstart | right start
rend | right end
nSites | Number of `refJunctions` (transcripts) that contain this site.
gene_id | Gene identifier.
strand | Strand on which gene resides.
fexid | Id value of first `refJunction` with coordinates.
cnNmd | Number of `refJunctions` whose transcript_biotype is not `nonsense_mediated_decay`.

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## A) Ensembl
    ##-------------------------------------##
    ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ef)
    enj <- getSpliceTable(ens)
    ufe <- unifyJuncs(enj)

    saveGenome(enj, "enj.RData", useBasedir=FALSE)
    enjr <- loadGenome("enj.RData")

    ##-------------------------------------##
    ## B) UCSC
    ##-------------------------------------##
    uf <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(uf)
    ucj <- getSpliceTable(uc)
    ufu <- unifyJuncs(ucj)

    saveGenome(ucj, "ucj.RData", useBasedir=FALSE)
    ucjr <- loadGenome("ucj.RData")

[Package refGenome version 1.7.7 Index]