gseaModule

length,GeneSet-method

An object of class
    <code><a href="/link/GeneSetCollection?package=cellHTS&version=1.42.0&to=GSEABase%3AGeneSetCollection-class" rd-options="GSEABase:GeneSetCollection-class" data-mini-rdoc="GSEABase:GeneSetCollection-class::GeneSetCollection">GeneSetCollection</a></code>
    containing the information about gene sets for which to perform the
    analysis.

geneSets

A list of functions to compute per gene set
    statistics. These will be called by
    <code><a href="/link/applyByCategory?package=cellHTS&version=1.42.0&to=Category%3AapplyByCategory" rd-options="Category:applyByCategory" data-mini-rdoc="Category:applyByCategory::applyByCategory">applyByCategory</a></code> and need to
    be able to handle two mandatory arguments: <code>x</code> are the scores
    for the respective category, and <code>y</code> are all scores of the
    whole assay. This allows for statistics like <code>t.test(x,y)</code>.

statFuns

An optional numeric vector of assay scores. This
      should be extended to also handle numeric matrices for multi-channel
      assays.

scores

A <code>data.frame</code> with additional annotation for the
      repsective gene sets.

annotation

gseaModule objects encapsulate all the information that is necessary to
add the results of a gene set enrichment analysis to a cellHTS
report. This feature is still experimental

Analysis of cell-based RNA interference screens.

Andrzej Ole

cellHTS

Analysis of cell-based screens

gseaModule function

An object of class
    <code><a href="GeneSetCollection" rd-options="GSEABase:GeneSetCollection-class">GeneSetCollection</a></code>
    containing the information about gene sets for which to perform the
    analysis.

A list of functions to compute per gene set
    statistics. These will be called by
    <code><a href="applyByCategory" rd-options="Category:applyByCategory">applyByCategory</a></code> and need to
    be able to handle two mandatory arguments: <code>x</code> are the scores
    for the respective category, and <code>y</code> are all scores of the
    whole assay. This allows for statistics like <code>t.test(x,y)</code>.

gseaModule: Constructor for an object of class gseaModule

Description

Usage

Arguments

Value

Details