export_for_iSEE {GeneTonic} | R Documentation

## export_for_iSEE

### Description

Combine data from a typical DESeq2 run

### Usage

    export_for_iSEE(dds, res_de, gtl = NULL)

### Arguments

`dds` | A `DESeqDataSet` object.
`res_de` | A `DESeqResults` object.
`gtl` | A `GeneTonic`-list object, containing in its slots the arguments specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names of the list must be specified following the content they are expecting

### 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 and/or after exploring the functional enrichment results with `GeneTonic()`

### 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 - mainly the results for differential expression analysis.

### Examples

    library("macrophage")
    library("DESeq2")

    # dds object
    data("gse", package = "macrophage")
    dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
    rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
    dds_macrophage <- estimateSizeFactors(dds_macrophage)

    # res object
    data(res_de_macrophage, package = "GeneTonic")
    res_de <- res_macrophage_IFNg_vs_naive

    # now everything is in place to launch the app
    # dds_macrophage <- DESeq2::DESeq(dds_macrophage)
    se_macrophage <- export_for_iSEE(dds_macrophage, res_de)
    # iSEE(se_macrophage)

[Package GeneTonic version 1.4.1 Index]