groupTestByGeneOntology: Run DISCOVER group-wise tests on gene sets defined by gene...
In connorH982/driverAnalytics: Visualize and Analyze results from the DISCOVER test
Description
This implements the discover group wise tests of exclusivity, coverage and impurity "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1114-x".
Automatically implements a the Benjamini-Hochberg multiple testing correction.
Usage
1
2
groupTestByGeneOntology(events, dictionary = NULL, go.type = "bp",
group.test.type = "exclusivity")
Arguments
events
Can either be a discover matrix that results from running the discover.pairwise.test() or an indicator matrix. If it is an indicator matrix, the function will run the discover test, but this will significantly increase execution time.
dictionary
If a dictionary object (makeDictionary) is not supplied this function will automatically generate one, though this increases execution time.
go.type
Character. Can be "bp","cc" or "mf" for biological process, cellular component, or molecular function respectively. Defaults to "bp"
group.test.type
The type of group test to be employed: "exclusivity", "coverage" or "impurity"
connorH982/driverAnalytics documentation built on May 23, 2019, 8:55 a.m.
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Description
This implements the discover group wise tests of exclusivity, coverage and impurity "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1114-x". Automatically implements a the Benjamini-Hochberg multiple testing correction.
Usage
1 2 | groupTestByGeneOntology(events, dictionary = NULL, go.type = "bp",
group.test.type = "exclusivity")
|
Arguments
events |
Can either be a discover matrix that results from running the discover.pairwise.test() or an indicator matrix. If it is an indicator matrix, the function will run the discover test, but this will significantly increase execution time. |
dictionary |
If a dictionary object ( |
go.type |
Character. Can be "bp","cc" or "mf" for biological process, cellular component, or molecular function respectively. Defaults to "bp" |
group.test.type |
The type of group test to be employed: "exclusivity", "coverage" or "impurity" |
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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