Description Usage Arguments Value Note
View source: R/FindPathwayEnrichment.R
Find Reactome pathways enriched from proximal binding
1 2 | FindPathwayEnrichment(distanceFrame, geneSet = NULL, minPathwayGenes = 5,
numCores = 4)
|
distanceFrame |
A dataframe resulting from the output of the GeneToPeakDist function. Should have two columns with the first having ENSEMBL gene IDs and the second the distance to the nearest ChIP peak. |
geneSet |
A character vector of ENSEMBL gene IDs to perform enrichment for proximal binding analysis on. If NULL, pathway analysis on all reactome pathways will be used for analysis. Defaults to NULL. |
minPathwayGenes |
A numeric indicating the minimum number of genes in a pathway required for inclusion in pathway analysis. Defaults to 5. |
numCores |
A numeric indicating the number of cores the function can use via R's parallel package. Defaults to 4. |
Returns a vector of one-sided Wilcoxon p-values with the alternate hypothesis of pathway genes enriched for shorter distances to the nearest ChIP-peak relative to all non-pathway genes.
Reactome
Terms of Use: http://www.reactome.org/pages/about/license-agreement/
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