isoDE: Differential expression analysis with DESeq2

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Differential expression analysis with DESeq2

Description

This function does differential expression analysis with DESeq2::DESeq2-package using the specific formula. It will return a DESeq2::DESeqDataSet object.

Usage

isoDE(ids, formula = NULL, ...)

Arguments

ids	Object of class IsomirDataSeq.
formula	Formula used for DE analysis.
...	Options to pass to isoCounts() including ref, iso5, iso3, add, subs and seed parameters.

Details

First, this function collapses all isomiRs in different types. Read more at isoCounts() to know the different options available to collapse isomiRs.

After that, DESeq2::DESeq2-package is used to do differential expression analysis. It uses the count matrix and design experiment stored at (counts(ids) and colData(ids)) IsomirDataSeq object to construct a DESeq2::DESeqDataSet object.

Value

DESeq2::DESeqDataSet object. To get the differential expression isomiRs, use DESeq2::results() from DESeq2 package. This allows to ask for different contrast without calling again isoDE(). Read results manual to know how to access all the information.

Examples

data(mirData)
ids <- isoCounts(mirData, minc=10, mins=6)
dds <- isoDE(mirData, formula=~condition)

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.