massiveGST {massiveGST} | R Documentation |
massive Gene-Sets Test with Mann-Whitney-Wilcoxon statistics.
Description
Perform a competitive gene set enrichment analysis by applying the Mann-Withney-Wilcoxon test.
Usage
massiveGST(gene_profile, gene_sets,
cols_to_remove = NULL,
alternative = c("two.sided", "less", "greater")
)
Arguments
gene_profile |
a named list of values; the names have to match the names of genes in the gene-set. |
gene_sets |
a character vector of gene-sets. |
cols_to_remove |
a list of colnames to eventually remove from the output. |
alternative |
a character string specifying the alternative hypothesis of the MWW test; must be one of "two.sided" (default), "greater" or "less". |
Value
A data frame with columns
size |
Original size of the gene-set. |
actualSize |
Size of the gene-set after the match with the gene-profile. |
NES |
(Normalized Enrichment Score) the strength of the association of the gene-set with the gene profile; also the percentile rank of the gene-set in the universe of the genes ouside the gene-set. |
odd |
odd transformation of the NES. |
logit2NES |
logit transformation of the NES. |
abs_logit2NES |
absolute value of the logit2NES in the case of "two.sided" alternative. |
p.value |
p-values associated with the gene-set. |
BH.value |
Benijamini and Hockberg adjustment of the p.values. |
B.value |
Bonferroni adjustment of the p.values. |
relevance |
marginal ordering of the table. |
Author(s)
Stefano M. Pagnotta
References
Cerulo, Pagnotta (2022) doi:10.3390/e24050739
See Also
summary.mGST, plot.mGST, cut_by_logit2NES, cut_by_NES, cut_by_significance
Examples
library(massiveGST)
# get the gene profile
fname <- system.file("extdata", package="massiveGST")
fname <- file.path(fname, "pre_ranked_list.txt")
geneProfile <- get_geneProfile(fname)
# get the gene-sets
geneSets <- get_geneSets_from_msigdbr(category = "H", what = "gene_symbol")
# run the function
ans <- massiveGST(geneProfile, geneSets, alternative = "two.sided")
ans