refGenome (version 1.7.7)

unifyJuncs: 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.

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.

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.

Examples

# NOT RUN {
##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
ufe <- unifyJuncs(enj)
# }
# NOT RUN {
saveGenome(enj, "enj.RData", useBasedir=FALSE)
enjr <- loadGenome("enj.RData")
# }
# NOT RUN {
##-------------------------------------##
## B) UCSC
##-------------------------------------##
uf <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(uf)
ucj <- getSpliceTable(uc)
ufu <- unifyJuncs(ucj)
# }
# NOT RUN {
saveGenome(ucj, "ucj.RData", useBasedir=FALSE)
ucjr <- loadGenome("ucj.RData")
# }