oranges: ORANGES: Over-Representation ANalysis for Gene Expression...
In diogocamacho/oranges: Over-representation analyses for human gene sets
Description
Usage
Arguments
Value
Description
oranges returns the enrichment of pathway sets given a query gene signature based on Fisher's exact test. Currently this function is built around enrichment of human pathway sets, but ora function can be generalized to fit different organisms of interest provided a pathway matrix is provided.
Usage
1
oranges(query_entrez, universe_entrez)
Arguments
universe_entrez
Full EntrezID set where the query set comes from (usually the full set of RNA-seq or microarray genes characterized in the transcriptomics platform)
query_set
Gene signature of interest, as EntrezIDs
universe_symbols
Gene symbols for the entire set of genes in universe
Value
A tibble.
diogocamacho/oranges documentation built on June 6, 2019, 11:52 p.m.
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Description Usage Arguments Value
Description
oranges returns the enrichment of pathway sets given a query gene signature based on Fisher's exact test. Currently this function is built around enrichment of human pathway sets, but ora function can be generalized to fit different organisms of interest provided a pathway matrix is provided.
Usage
1 | oranges(query_entrez, universe_entrez)
|
Arguments
universe_entrez |
Full EntrezID set where the query set comes from (usually the full set of RNA-seq or microarray genes characterized in the transcriptomics platform) |
query_set |
Gene signature of interest, as EntrezIDs |
universe_symbols |
Gene symbols for the entire set of genes in universe |
Value
A tibble.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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