gseaModule

length,GeneSet-method

An object of class
    <code><a rd-options="GSEABase:GeneSetCollection-class" href="/link/GeneSetCollection?package=cellHTS2&version=2.36.0&to=GSEABase%3AGeneSetCollection-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 rd-options="Category:applyByCategory" href="/link/applyByCategory?package=cellHTS2&version=2.36.0&to=Category%3AapplyByCategory" 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


This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.

Joseph Barry

cellHTS2

Analysis of cell-based screens - revised version of cellHTS

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>.

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

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

gseaModule: Constructor for an object of class gseaModule

Description

Usage

Arguments

Value

Details