enrichment {ACSNMineR}R Documentation

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:

module

The name of the map or the module preceded by the map

module_size

The number of genes in the module after taking into account universe reduction

nb_genes_in_module

The number of genes from input list in the module

genes_in_module

Names of the genes from input list in the module, space separated

universe_size

size of the input universe

nb_genes_in_universe

number of genes from the input list that are found in the universe

test

the kind of test that was looked for. "greater" when enrichment is tested, "less" when depletion is tested, or "two.sided"

Examples

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

[Package ACSNMineR version 0.16.8.25 Index]