Description Usage Arguments Value Examples
Automated gene set analysis for multiple sets
1 2 3 4 5 6 | 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:
The name of the map or the module preceded by the map
The number of genes in the module after taking into account universe reduction
The number of genes from input list in the module
Names of the genes from input list in the module, space separated
size of the input universe
number of genes from the input list that are found in the universe
the kind of test that was looked for. "greater" when enrichment is tested, "less" when depletion is tested, or "two.sided"
1 2 3 4 | 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)
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