CDSSet: Container for coding sequence (CDS) annotation information

Description Usage Arguments Details Value Author(s) References

View source: R/tools.R

Description

A container for coding sequence annotation information.

Usage

1
CDSSet(cds)

Arguments

cds

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

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 analyzeORF). strand, the strand, cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issues), and cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issues).

The CDSset object is used with analyzeORF if annotated TSS should be analyzed.

For an example, see getCDS.

Value

A CDSSet object.

Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

References

Vitting-Seerup K, et al: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014, 15:81.


kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.