readDESeqDs: Read a DESeqDataset

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Read a DESeqDataset

Description

readDESeqDs reads file of PACs or genes into a DESeqDataset.

Usage

readDESeqDs(datafile, annofile, filetype, noIntergenic = TRUE, PAname = NULL)

Arguments

datafile	a gene/PA file.
annofile	annotation for samples.
filetype	specify the file type, gene/PA.
noIntergenic	valid when filetype=PA, specifying whether to remove intergenic PACs.
PAname	valid when filetype=PA, specifying how to set the name (rowname) of PACs. PAname=PA, the PA name is set as 'gene.PAN'; PAname=coord, then 'gene.coord'.

Value

A DESeqDataset with each row a gene or PAC.

Examples

data(PACds)
writePACds(PACds, file='pacds.txt', colDataFile='coldata.txt')

## Read PACs to DESeqDataset
dds=readDESeqDs(datafile='pacds.txt', annofile='coldata.txt',
     filetype='PA',noIntergenic=TRUE, PAname='PA')
head(mcols(dds)); colData(dds); head(assays(dds)$counts)

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.