isoDE {isomiRs} | R Documentation

## 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)

[Package isomiRs version 1.14.0 Index]