isoformProportions {fishpond} | R Documentation

## Create isoform proportions from scaled data

### Description

Takes output of scaled (and optionally filtered) counts and returns isoform proportions by dividing out the total scaled count for the gene for each sample. The operation is performed on the `counts` assay, then creating a new assay called `isoProp`, and on all of the inferential replicates, turning them from counts into isoform proportions. Any transcripts (rows) from single isoform genes are removed, and the transcripts will be re-ordered by gene ID.

### Usage

    isoformProportions(y, geneCol = "gene_id", quiet = FALSE)

### Arguments

`y` | a SummarizedExperiment
`geneCol` | the name of the gene ID column in the metadata columns for the rows of `y`
`quiet` | display no messages

### Value

a SummarizedExperiment, with single-isoform transcripts removed, and transcripts now ordered by gene

[Package fishpond version 1.4.1 Index]