addIsCoding: Add information on coding/non-coding status.
In refGenome: Gene and Splice Site Annotation Using Annotation Data from 'Ensembl' and 'UCSC' Genome Browsers
Description
Usage
Arguments
Author(s)
Examples
Description
The addIsCoding method extracts positions from 'CDS'
features in the ensemblGenome object.
The positions of the 'CDS' features are compared with the splice-junction
positions in the ensemblJunctions object. When a match is found,
the splice junction is marked as coding, otherwise the junction is marked as
non-coding.
The coding information is calculated for each flanking exon of the
splice-junction.
The column name for the left side (lend) is licd, the name for the
right side (rstart) is ricd.
Usage
1
addIsCoding(object,ens)
Arguments
object
ensemblJunctions.
The object to which isCoding columns are added.
ens
ensemblGenome.
Genome object which should contain 'CDS' features.
Author(s)
Wolfgang Kaisers
Examples
1
2
3
4
ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
addIsCoding(enj, ens)
refGenome documentation built on May 23, 2019, 1:03 a.m.
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Description Usage Arguments Author(s) Examples
Description
The addIsCoding method extracts positions from 'CDS'
features in the ensemblGenome object.
The positions of the 'CDS' features are compared with the splice-junction
positions in the ensemblJunctions object. When a match is found,
the splice junction is marked as coding, otherwise the junction is marked as
non-coding.
The coding information is calculated for each flanking exon of the
splice-junction.
The column name for the left side (lend) is licd, the name for the
right side (rstart) is ricd.
Usage
1 | addIsCoding(object,ens)
|
Arguments
object |
|
ens |
|
Author(s)
Wolfgang Kaisers
Examples
1 2 3 4 | ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
addIsCoding(enj, ens)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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