PDseDataSet-class {PAIRADISE}R Documentation

PDseDataSet object and constuctor

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)

[Package PAIRADISE version 1.9.0 Index]