addCDS: Add CDS to rowRanges of a transcript-level...

In mikelove/tximeta: Transcript Quantification Import with Automatic Metadata

Add CDS to rowRanges of a transcript-level SummarizedExperiment

Description

Working similarly to addExons, this function can be used to add information about CDS (coding sequence) to the SummarizedExperiment object. As not all transcripts are coding, we have CDS information for only a subset of the rows of the object. For this reason, a logical indicator for whether the transcript is coding, mcols(se)$coding, is added as a column to the metadata columns of the rowRanges of the object. An additional column, mcols(se)$cds, is added to the metadata columns, which is a GRangesList with either the CDS regions (if the transcript is coding), or the original transcript/exon ranges (if the transcript is non-coding). This is necessary, as GRangesList cannot have NA elements. As with addExons, this function is designed only for transcript-level objects.

Usage

addCDS(se)

Arguments

se	the SummarizedExperiment

Value

a SummarizedExperiment

mikelove/tximeta documentation built on Oct. 21, 2024, 5:46 a.m.