summarizeToGene,SummarizedExperiment-method {tximeta}R Documentation

Summarize estimated quantitites to gene-level

Description

Summarizes abundances, counts, lengths, (and inferential replicates or variance) from transcript- to gene-level. 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

Examples


example(tximeta)
gse <- summarizeToGene(se)


[Package tximeta version 1.2.1 Index]