wrapup_for_iSEE {ideal} | R Documentation

## wrapup_for_iSEE

### Description

Combine data from a typical DESeq2 run

### Usage

    wrapup_for_iSEE(dds, res)

### Arguments

`dds` | A `DESeqDataSet` object.
`res` | A `DESeqResults` object.

### Details

Combines the DESeqDataSet input and DESeqResults into a SummarizedExperiment object, which can be readily explored with iSEE.

A typical usage would be after running the DESeq2 pipeline as specified in one of the workflows which include this package, e.g. in the context of the ideal package.

### Value

A SummarizedExperiment object, with raw counts, normalized counts, and variance-stabilizing transformed counts in the assay slots; and with colData and rowData extracted from the corresponding input parameters

### Examples

    # with simulated data...
    library(DESeq2)
    dds <- DESeq2::makeExampleDESeqDataSet(n = 10000, m = 8)
    dds <- DESeq(dds)
    res <- results(dds)
    se <- wrapup_for_iSEE(dds, res)
    # library(iSEE)
    # iSEE(se)
    ## Not run:
    # or with the well known airway package...
    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
      colData = colData(airway),
      design = ~ cell + dex
    )
    dds_airway <- DESeq2::DESeq(dds_airway)
    res_airway <- DESeq2::results(dds_airway)
    se_airway <- wrapup_for_iSEE(dds_airway, res_airway)
    # iSEE(se_airway)

    ## End(Not run)

[Package ideal version 1.18.1 Index]