ideal {ideal} | R Documentation

## ideal: Interactive Differential Expression Analysis

### Description

ideal makes differential expression analysis interactive, easy and reproducible. This function launches the main application included in the package.

### Usage

    ideal(
      dds_obj = NULL,
      res_obj = NULL,
      annotation_obj = NULL,
      countmatrix = NULL,
      expdesign = NULL,
      gene_signatures = NULL
    )

### Arguments

`dds_obj` | A `DESeqDataSet` object. If not provided, then a `countmatrix` and a `expdesign` need to be provided. If none of the above is provided, it is possible to upload the data during the execution of the Shiny App
`res_obj` | A `DESeqResults` object. If not provided, it can be computed during the execution of the application
`annotation_obj` | A `data.frame` object, with row.names as gene identifiers (e.g. ENSEMBL ids) and a column, `gene_name`, containing e.g. HGNC-based gene symbols. If not provided, it can be constructed during the execution via the org.eg.XX.db packages - these need to be installed
`countmatrix` | A count matrix, with genes as rows and samples as columns. If not provided, it is possible to upload the data during the execution of the Shiny App
`expdesign` | A `data.frame` containing the info on the covariates of each sample. If not provided, it is possible to upload the data during the execution of the Shiny App
`gene_signatures` | A list of vectors, one for each pathway/signature. This is for example the output of the `read_gmt` function. The provided object can also be replaced during runtime in the dedicated upload widget.

### Value

A Shiny App is launched for interactive data exploration and differential expression analysis

### Examples

    # with simulated data...
    library(DESeq2)
    dds <- DESeq2::makeExampleDESeqDataSet(n = 100, m = 8)
    cm <- counts(dds)
    cd <- colData(dds)

    # with the well known airway package...
    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
      colData = colData(airway),
      design = ~ cell + dex
    )
    ## Not run:

    ideal()
    ideal(dds)
    ideal(dds_airway)

    dds_airway <- DESeq2::DESeq(dds_airway)
    res_airway <- DESeq2::results(dds_airway)
    ideal(dds_airway, res_airway)

    ## End(Not run)

[Package ideal version 1.18.1 Index]