enrichment: Gene set enrichment analysis

In ACSNMineR: Gene Enrichment Analysis from ACSN Maps or GMT Files

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")

Example output

Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: scales
             module module_size nb_genes_in_module
1         cellcycle         228                 12
V11 APOPTOSIS_ENTRY          10                  4
V12            E2F1          19                 12
V18    E2F6_TARGETS          34                  2
                                                            genes_in_module
1   ATM ATR CHEK2 CREBBP TFDP1 E2F1 EP300 HDAC1 KAT2B GTF2H1 GTF2H2 GTF2H2B
V11                                                      ATM ATR CHEK2 E2F1
V12 ATM ATR CHEK2 CREBBP TFDP1 E2F1 EP300 HDAC1 KAT2B GTF2H1 GTF2H2 GTF2H2B
V18                                                              CHEK2 E2F1
    universe_size nb_genes_in_universe      p.value p.value.corrected    test
1            2240                   12 2.897631e-07      1.282434e-06 greater
V11          2240                   12 3.497547e-07      1.282434e-06 greater
V12          2240                   12 3.675956e-21      4.043552e-20 greater
V18          2240                   12 1.764878e-02      4.853414e-02 greater

ACSNMineR documentation built on May 1, 2019, 9:14 p.m.