The DeeDeeExperiment class

The DeeDeeExperiment class is integrate and manage transcriptomic analysis results. It inherits from the SummarizedExperiment class, and additionally stores DE-related/functional enrichment information via dedicated slots and colData.

Usage

DeeDeeExperiment(se = NULL, de_results = NULL, enrich_results = NULL)

Arguments

se

A SummarizedExperiment object, that will be used as a scaffold to store the DE related information.

de_results

A named list of DE results, in any of the formats supported by the package (currently: results from DESeq2, edgeR, limma).

enrich_results

A named list of functional enrichment results. Each element can be either a data.frame (currently supports results from topGO, enrichR, gProfiler, fgsea, gsea, DAVID, and output of GeneTonic shakers), or an enrichResult/gseaResult objects (currently supports clusterProfiler)

Value

A DeeDeeExperiment object.

Details

The se parameter can be optionally left unspecified. If this is the case, the resulting DeeDeeExperiment object will contain as features the ones specified by the provided components of the object supplied via the de_results parameter.

The conversion of the components of the de_results list will be handled via conversion functions to uniform the names and set of information which will be stored in the returned DeeDeeExperiment object. The names of the list will be used to define the contrasts for the different DE analyses included, which will determine the way to access the information stored in the dea slot of the DeeDeeExperiment object.

The content of the enrich_results provided by the user will be validated to ensure that it is properly formatted and correctly named. The FE tool can be automatically detected, and based on that, the appropriate shaking method is used to return a standardized format of the FEA results. The names of the list will be used to attempt to associate each enrichment result with a corresponding DE contrast stored in the DeeDeeExperiment object.

Since a DeeDeeExperiment is also a SummarizedExperiment object, it can be seamlessly provided downstream for visualization and in-depth exploration to packages such as iSEE or similar.

Slots

dea

This slot is designed to hold the DE-related information. This is internally being created upon importing from the list of DE results objects, provided when instantiating the DeeDeeExperiment.

fea

This slot is designed to hold Functional Enrichment related information.

Author

Najla Abassi, Lea Rothörl, and Federico Marini

Examples

data("de_named_list", package = "DeeDeeExperiment")

dde_onlyde <- DeeDeeExperiment(
  de_results = de_named_list
)
#> ℹ creating a mock SE from the rows of the DE result objects, if available

# or, with a SE object as support - even without assay data available
library("SummarizedExperiment")

rd_macrophage <- DataFrame(
  gene_id = rownames(de_named_list$ifng_vs_naive)
)
rownames(rd_macrophage) <- rownames(de_named_list$ifng_vs_naive)
se_macrophage_noassays <- SummarizedExperiment(
  assays = SimpleList(),
  rowData = rd_macrophage
)

dde <- DeeDeeExperiment(
  se_macrophage_noassays,
  de_results = de_named_list
)