multisample_enrichment: Automated gene set analysis for multiple sets
In ACSNMineR: Gene Enrichment Analysis from ACSN Maps or GMT Files

Description Usage Arguments Value Examples

Automated gene set analysis for multiple sets

multisample_enrichment(Genes_by_sample = 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, cohort_threshold = TRUE,
  alternative = "greater")

`Genes_by_sample`	List of character vectors. Each list element name should be a sample name, and each character vector the set of genes to test for the sample.
`maps`	list of maps generated by format_from_gmt. Default: tests on all acsn maps
`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
`cohort_threshold`	if TRUE modules will be kept in all samples if at least one sample has p-value lower than threshold, otherwise the threshold is applied for each sample independently.
`alternative`	One of "greater", "less", "both", or "two.sided" (only for fisher test). Greater will check for enrichment, less will check for depletion, and both will look for both.

Output is a list of dataframes with names the names given in 'Genes_by_sample' 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"

multisample_enrichment(Genes_by_sample = list(set1 = genes_test,set2=c(genes_test,"PTPRD")),
maps = list(cellcycle = ACSNMineR::ACSN_maps$CellCycle),
min_module_size = 10,
universe = "ACSN",cohort_threshold = FALSE)