isoformProportions: Create isoform proportions from scaled data

In fishpond: Fishpond: differential transcript and gene expression with inferential replicates

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

fishpond documentation built on Nov. 8, 2020, 7:54 p.m.