DEET_Input_as_Reference {DEET}

DEET_Input_as_Reference

Description

Alternative function to DEET enrich for when the inputted gene list is unordered. Here, we can increase the statistical rigour of enrichment by levaraging the p-values of the DEGs within DEET. Specifically, the inputted DE list is used as the reference and we test each DE list against your reference. Specifically. We convert your reference into a gmt file before inputting each pairwise DE list into ActivePathways. This function does not complete correlations or pathway-level analysis.

Usage

DEET_Input_as_Reference(genes, DEET_dataset, background = NULL)

Arguments

genes

A character vector of gene symbols within 'DEET_dataset'

DEET_dataset

The databank of the differential expression enrichment tool. Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y. The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data. Unlike in DEET_enrich, this dataset does not require the pathway-relevant elements of the DEET_dataset list, namely "gmt_BP", or "gmt_TF" "DEET_gmt_BP", "DEET_gmt_TF". It also does not need DEET_gmt_DE.

background

Character vector of human gene symbols showing all possible genes. Default value is NULL and the background is generated as all detected DEGs across any comparison.

Value

Named list containing the ActivePathways enrichment of each comparison on the user's inputted gene list, as well as the associated metadata of each enriched comparison.

Author(s)

Dustin Sokolowski

References

Paczkowska M, Barenboim J, Sintupisut N, et al. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020;11(1):735. doi:10.1038/s41467-019-13983-9

Examples

data("example_DEET_enrich_input")
genes <- rownames(example_DEET_enrich_input)
data("DEET_example_data")
DEET_out_ref <- DEET_Input_as_Reference(genes, DEET_dataset = DEET_example_data)