spliceR (version 1.14.0)

CDSSet: Container for coding sequence (CDS) annotation information

Description

A container for coding sequence annotation information.

Usage

CDSSet(cds)

Arguments

cds

A data.frame object contaning CDS annotation. See details for required columns.

Value

A CDSSet object.

Details

This object can be generated automatically from getCDS, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:

chrom, the chromosome name (NB: chromosome names must match when running annotatePTC). strand, the strand, cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issuses), and cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issuses).

The CDSset object is required by annotatePTC for translation of transcripts and premature termination codon annotation.

For an example, see annotatePTC.

References

Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.