enrichment: Gene set enrichment analysis

Description

Compute and represent gene set enrichment from your data based on pre-saved maps from ACSN or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.

Usage

enrichment(Genes = NULL, maps = c("Apoptosis", "CellCycle", "DNA_repair", "EMT_motility", "Survival"), correction_multitest = "BH", statistical_test = "fisher", min_module_size = 5, universe = "map_defined", Remove_from_universe = NULL, threshold = 0.05, alternative = "greater")

Arguments

Genes

Character vector of genes that should be tested for enrichment

maps

list of maps generated by format_from_gmt. Names of element of list will be used to track modules. Default: tests on the master map.

correction_multitest

either FALSE, "bonferroni", "holm", "hochberg", "hommel", "BH", "fdr" (identical to BH), or "BY"

statistical_test

one of "fisher", "hypergeom"

min_module_size

will remove from the analysis all modules which are (strictly) smaller than threshold

universe

Universe on which the statistical analysis should be performed. Can be either "HUGO","ACSN","map_defined", or a character vector of genes.

Remove_from_universe

Default is NULL. A list of genes that should not be considered for enrichment (will be removed from input, maps, and universe). The size of universe and map will be updated after removal.

threshold

maximal p-value (corrected if correction is enabled) that will be displayed

alternative

One of "greater", "less", "both" or "two.sided" Greater will check for enrichment, less will check for depletion, and both will look for both and will keep track of the side, while two-sided (only for fisher test) checks if there is a difference.

Value

Output is a dataframe with the following columns:

Examples

Run this code

enrichment(genes_test,min_module_size = 10, 
   threshold = 0.05,
   maps = list(cellcycle = ACSNMineR::ACSN_maps$CellCycle),
   universe = "ACSN")

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