ccData

gseaRes

gUniverse

table10

table48

enrichLists

ccResults

ccResultsBPHier

ccOpts

geneLists

Processed data from the <code>estrogen</code> example data set

datasets

Calculates significant annotations (categories) in each of
two (or more) feature (i.e. gene) lists, determines the overlap
between the annotations, and returns graphical and tabular data
about the significant annotations and which combinations of
feature lists the annotations were found to be significant.
Interactive exploration is facilitated through the use of
RCytoscape (heavily suggested).

Robert M Flight

categoryCompare

Meta-analysis of high-throughput experiments using feature
annotations

ccData function

<code>table10</code>: Log-ratio output from limma for the comparison of presence-absence of estrogen at 10 hours <code>table48</code>: Log-ratio output from limma for the comparison of presence-absence of estrogen at 48 hours <code>gUniverse</code>: All of the genes measured on the chip <code>gseaRes</code>: Toy results of GSEA analysis of 3 different tissues <code>enrichLists</code>: Apply <code><a rd-options="" href="/link/ccEnrich?package=categoryCompare&version=1.16.2" data-mini-rdoc="categoryCompare::ccEnrich">ccEnrich</a></code> to a ccGeneList from <code>table10</code> and <code>table48</code> <code>ccResults</code>: Apply <code><a rd-options="" href="/link/ccCompare?package=categoryCompare&version=1.16.2" data-mini-rdoc="categoryCompare::ccCompare">ccCompare</a></code> to <code>enrichLists</code> <code>ccResultsBPHier</code>: Modify <code>enrichLists$BP</code> to use a "hierarchical" layout <code>geneLists</code>: a <code>ccGeneList</code> generated from genes in table10 and table48 <code>ccOpts</code>: a <code>ccOptions</code> object describing what we are going to do as far as feature list comparisons

Format

Taken from the estrogen package in Bioconductor, and then processed using the normal affy and limma tools.

Source

Processed data from the <code>estrogen</code> example data set

ccData: Test data for `categoryCompare`

Description

Usage

Arguments

Format

Source

See Also

Examples