ideal: ideal: Interactive Differential Expression Analysis

In federicomarini/ideal: Interactive Differential Expression AnaLysis

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 DESeq2::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 DESeq2::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", package = "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)

federicomarini/ideal documentation built on Dec. 21, 2024, 8:46 p.m.