evalClusterHyper {goCluster} | R Documentation |
The function evalClusterHyper
moves through a tree of gene groups and
calls the function evalAnnosetHyper
for each of them. This second
function employs the hypergeometric distributon to calculate a p-value
for each of the annotation terms that is annotated to the genes in the
group.
evalClusterHyper(X, uniqueid, Annoset) evalAnnosetHyper(Selection, uniqueid, Annoset)
X |
The tree (list of lists) of clusters. |
Annoset |
This is a list with each element holding a different annotation dataset. Each of this dataset is composed of two columns with the first column matching the ids of the genes given in the clusters, while the second column holds the corresponding annotation terms. |
uniqueid |
The unique id of the elements in the dataset. |
Selection |
A list of genes that comprise one cluster. The ids given here have to match the ids from the first column of the annotation dataterms. |
This class uses a "tree" (list of lists) of gene groups and analyzes the frequency of associated annotation terms within these groups using the hypergeometric distribution. For each group the unique annotation terms will be extracted and all genes matching these terms are selected as a reference set. The algorithm will then use the hypergeometric distribution to determine for each available annotation term in that group whether the genes in the group that match this term are enriched in this
pvalues |
Description of 'comp1' |
selectedPerAnnotation |
A vector that holds the number of times the annotation was found in the given selection. |
elementsPerAnnotation |
A vector that holds the number of times the annotation was found over all elements. |
selectedTotal |
Total number of annotation terms in the given selection. |
elementsTotal |
Total number of annotation terms over all elements. |
Gunnar Wrobel, http://www.gunnarwrobel.de.
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