summarizeToGene: Summarize estimated quantitites to gene-level

In tximeta: Transcript Quantification Import with Automatic Metadata

Description

Summarizes abundances, counts, lengths, (and inferential replicates or variance) from transcript- to gene-level. Transcript IDs are stored as a CharacterList in the mcols of the output object. This function operates on SummarizedExperiment objects, and will automatically access the relevant TxDb (by either finding it in the BiocFileCache or by building it from an ftp location). This function uses the tximport package to perform summarization, where a method is defined that works on simple lists.

Usage

## S4 method for signature 'SummarizedExperiment'
summarizeToGene(object, varReduce = FALSE, ...)

Arguments

object	a SummarizedExperiment produced by tximeta
varReduce	whether to reduce per-sample inferential replicates information into a matrix of sample variances variance (default FALSE)
...	arguments passed to tximport

Value

a SummarizedExperiment with summarized quantifications and transcript IDs as a CharacterList in the mcols

Examples

example(tximeta)
gse <- summarizeToGene(se)

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