Description Usage Arguments Value Examples
Simple fisher's exact test for enrichment in a given set of genes of interest (Goi)
1 2 | testEnrichment(Goi, gsets, background, minknown = 2, mindiffexp = 2,
maxknown = 500)
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Goi |
character vector containing the genes tested for enrichment |
gsets |
List of character vectors, each containing a set of genes (gene identifiers) |
background |
character vector containing background gene identifiers |
minknown |
Minimal number of genes within a gene set for it to be considered for enrichment |
mindiffexp |
Minimal number of genes differentially expressed within a gene set for it to be considered for enrichment |
maxknown |
Maximal number of genes within a gene set for it to be considered for enrichment |
Dataframe containing for every gene set which passed the filtering:
p-value of enrichment
q-value of enrichment (p-value corrected for multiple testing)
estimated odds score of enrichment, how much more likely is a given gene set to be part of
1 2 3 4 | Goi = 1:50
gsets = list(a= 20:70, b = 45:80)
background = 1:100
testEnrichment(Goi, gsets, background)
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