PDseDataSet: PDseDataSet object and constuctor

In hubentu/PAIRADISE: PAIRADISE: Paired analysis of differential isoform expression

Description

'PDseDataSet' is a subclass of 'SummarizedExperiment'. It can used to store inclusion and skipping splicing counts for pair designed samples.

Usage

PDseDataSet(counts, design, lengths)

Arguments

counts	The counts of splicing events, including inclusion and skipping counts in 3 dimensions for each sample.
design	The paired design data.frame, including sample column for sample ids and group column for design factors.
lengths	Two columns iLen and sLen for the effective lengths of inclusion and skipping isoforms.

Value

A PDseDataSet object

Examples

icount <- matrix(1:4, 1)
scount <- matrix(5:8, 1)
acount <- abind::abind(icount, scount, along = 3)
design <- data.frame(sample = rep(c("s1", "s2"), 2),
group = rep(c("T", "N"), each = 2))
lens <- data.frame(sLen=1L, iLen=2L)
PDseDataSet(acount, design, lens)

hubentu/PAIRADISE documentation built on Oct. 4, 2020, 4:27 a.m.