refGenome (version 1.7.7)

refExons-class: Class "refExons"

Description

refExons represents genomic annotation data on exon-features for Ensembl and UCSC genomes. Relative locations of CDS, start_codon and stop_codon features are added. The unifiedExons class is intended to be used as preparation of exonic coordinates for counting of alignments (reads) inside these regions. In order to prevent ambiguities, overlaps are removed.

Objects from the Class

Objects can be created by calls of the form refExons(rg). 'rg' represents an object of class ensemblGenome or ucscGenome.

Slots

basedir:

Object of class "character" Directory where SQLite database is written.

%

ev:

Object of class "environment" Environment that contains data structures. Optionally, there are gtf and attr data.frames.

%

Methods

show

signature(object = "ensemblExons"): Creates a sensible printout.

%

getSpliceTable

signature(object = "ensemblExons", coding="logical"): Returns tabled splice sites. When coding=TRUE only entries with gene_biotype=="protein_coding" are included.

%

References

Ensembl File index

http://www.ensembl.org/info/data/ftp/index.html

GTF Field definitions

http://mblab.wustl.edu/GTF22.html#fields

UCSC home page

http://genome.ucsc.edu/

Examples

# NOT RUN {
##-------------------------------------##
## A) Ensembl
##-------------------------------------##
ensfile <- system.file("extdata",
                        "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ensfile)
enex <- refExons(ens)
# }
# NOT RUN {
saveGenome(enex,"enex.RData", useBasedir=FALSE)
er <- loadGenome("enex.RData")
# }
# NOT RUN {
# Unify exons
uex <- unifyRanges(enex)

##-------------------------------------##
## B) UCSC
##-------------------------------------##
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
ucex <- refExons(uc)
# }
# NOT RUN {
saveGenome(ucex, "ucex.RData", useBasedir=FALSE)
ur <- loadGenome("ucex.RData")
# }