addExons: Add exons to rowRanges of a transcript-level...

In tximeta: Transcript Quantification Import with Automatic Metadata

Description

After running tximeta, the SummarizedExperiment output will have GRanges representing the transcript locations attached as rowRanges to the object. These provide the start and end of the transcript in the genomic coordiantes, and strand information. However, the exonic locations are not provided. This function, addExons, swaps out the GRanges with a GRangesList, essentially a list along the rows of the SummarizedExperiment, where each element of the list is a GRanges providing the locations of the exons for that transcript.

Usage

addExons(se)

Arguments

se	the SummarizedExperiment

Details

This function is designed only for transcript-level objects. This "lack of a feature" reflects a belief on the part of the package author that it makes more sense to think about exons belonging to transcripts than to genes. For users desiring exonic information alongside gene-level objects, for example, which exons are associated with a particular gene, it is recommended to pull out the relevant GRangesList for the transcripts of this gene, while the object represents transcript-level data, such that the exons are still associated with transcripts.

For an example of addExons, please see the tximeta vignette.

Value

a SummarizedExperiment

tximeta documentation built on April 13, 2021, 6:01 p.m.