View source: R/GMT_enrichments.R
hypergeoTestForGeneset | R Documentation |
Gene list hypergeometric test against gmt format list of gene set. Can be used for custom pathway analysis or CMAP style query.
hypergeoTestForGeneset(query, refGMT, gspace, minGeneSet = 10, ef.psc = 0)
hypergeoTestForGeneset2(
query,
refGMT,
gspace,
minGeneSet = 10,
ncore = 1,
ef.psc = 0
)
query |
gene set to query (eg. Differentially Expressed Genes) |
refGMT |
list of reference gene set (eg. Pathways) |
gspace |
background gene space. Should contain all genes in query. |
minGeneSet |
minimum size of gene set. This is used to filter refGMT. Default 10 |
ef.psc |
pseudocount when calculating enrichment factor (oddsRatio). Default 0 |
ncore |
number of cores used in hypergeoTestForGeneset2 (soon to be removed) |
Data frame of gene set analysis results
: hypergeometric test p values from phyper
: -log10(p value)
: odds ratio
: tanimoto coefficient (Jaccard index)
: intersected item count
: gene set ratio (selected genes in gene set / selected genes)
: background ratio (total genes in gene set / total gene space)
hypergeoTestForGeneset2()
: Using multiprocessing (Deprecated)
gset <- c("A", "B", "C")
glist <- list(ID1 = LETTERS[1:10], ID2 = LETTERS[4:25])
hypergeoTestForGeneset(gset, glist, LETTERS)
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