summarizeToGene: Summarize estimated quantitites to gene-level

In mikelove/tximeta: Transcript Quantification Import with Automatic Metadata

Summarize estimated quantitites to gene-level

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,
  assignRanges = c("range", "abundant"),
  varReduce = FALSE,
  ...
)

Arguments

object	a SummarizedExperiment produced by tximeta
assignRanges	"range" or "abundant", this argument controls the way that the rowRanges of the output object are assigned (note that this argument does not affect data aggregation at all). The default is to just output the entire range of the gene, i.e. the leftmost basepair to the rightmost basepair across all isoforms. Alternatively, for expressed genes, one can obtain the start and end of the most abundant isoform (averaging over all samples). Non-expressed genes will have range-based positions. For abundant, for expressed genes, the name of the range-assigned isoform, max_prop (maximum isoform proportion), and iso_prop (numeric values for isoform proportions) are also returned in mcols
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)

mikelove/tximeta documentation built on Feb. 26, 2024, 4:32 a.m.