enrichmentTest

Takes a vector of names representing phosphorylation sites that are partitioned in the same cluster 
and an kinase-substrate annotation. Test for enrichment of the kinase based on the name vector.

CLUster Evaluation (CLUE) is a computational method for identifying
optimal number of clusters in a given time-course dataset clustered by
cmeans or kmeans algorithms and subsequently identify key kinases or
pathways from each cluster. Its implementation in R is called ClueR.
See README on <https://github.com/PYangLab/ClueR> for more details.
P Yang et al. (2015) <doi:10.1371/journal.pcbi.1004403>.

Pengyi Yang

ClueR

Cluster Evaluation

enrichmentTest function

<dl><dt>clust</dt>
<dd>a vector of names representing phosphorylation sites that are partitioned in the same cluster</dd>
<dt>annotation</dt>
<dd>a list with names correspond to kinases and elements correspond to substrates belong to each kinase</dd>
<dt>universe</dt>
<dd>the universe of names to compare against</dd>
<dt>alter</dt>
<dd>indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less"</dd></dl>

Arguments

Fisher's exact test-based enrichment test — enrichmentTest

<dl>

<dt>clust</dt>
<dd>a vector of names representing phosphorylation sites that are partitioned in the same cluster</dd>


<dt>annotation</dt>
<dd>a list with names correspond to kinases and elements correspond to substrates belong to each kinase</dd>


<dt>universe</dt>
<dd>the universe of names to compare against</dd>


<dt>alter</dt>
<dd>indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less"</dd>

</dl>

enrichmentTest: Fisher's exact test-based enrichment test

Description

Usage

Value

Arguments