annotate_eset_list


 A list of eSet objects, usually generated by a call to the <code><a rd-options="" href="/link/splitPerturbations?package=gCMAP&version=1.16.0" data-mini-rdoc="gCMAP::splitPerturbations">splitPerturbations</a></code> functions
 

eset.list


 The name of the pData column for eSets in 'eset.list' identifying treatment and control samples.
 

cmap.column


 The character string in the 'cmap.column' of the pData column for eSets in 'eset.list' identifying perturbation associated with treated samples.


perturbation


For each eSet in the 'eset.list', the pData slot is examined. Perturbation instances are identified as a match to 'perturbation' in the 'cmap.column' of the pData slot. The first matching row is extracted and transfered into the output data.frame, which contains one row for each eSet in the 'eset.list'. Only annotation columns found in the pData slots of all eSets in the 'eset.list' are returned.


The gCMAP package provides a toolkit for comparing
differential gene expression profiles through gene set
enrichment analysis. Starting from normalized microarray or
RNA-seq gene expression values (stored in lists of
ExpressionSet and CountDataSet objects) the package performs
differential expression analysis using the limma or DESeq
packages. Supplying a simple list of gene identifiers, global
differential expression profiles or data from complete
experiments as input, users can use a unified set of several
well-known gene set enrichment analysis methods to retrieve
experiments with similar changes in gene expression. To take
into account the directionality of gene expression changes,
gCMAPQuery introduces the SignedGeneSet class, directly
extending GeneSet from the GSEABase package.  To increase
performance of large queries, multiple gene sets are stored as
sparse incidence matrices within CMAPCollection eSets. gCMAP
offers implementations of 1. Fisher's exact test (Fisher, J R
Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al,
Science, 2006) 3. Parametric and non-parametric t-statistic
summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4.
Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon,
Biometrics Bulletin, 1945) as well as wrappers for the 5.
camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer
(Wu et al, Bioinformatics, 2010) functions from the limma
package and 7. wraps the gsea method from the mgsa package
(Bauer et al, NAR, 2010). All methods return CMAPResult
objects, an S4 class inheriting from AnnotatedDataFrame,
containing enrichment statistics as well as annotation data and
providing simple high-level summary plots.

Thomas Sandmann

gCMAP

Tools for Connectivity Map-like analyses

annotate_eset_list function


 A list of eSet objects, usually generated by a call to the <code><a rd-options='' href='splitPerturbations'>splitPerturbations</a></code> functions
 


Function to complile a data frame with per-instance annotation for a list of eSet objects generated by the <code><a rd-options='' href='splitPerturbations'>splitPerturbations</a></code> function. The output can be used directly as sample.annotation for the <code><a rd-options='' href='NChannelSet'>NChannelSet</a></code> function. 



Function to complile a data frame with per-instance annotation for a list of eSet objects generated by the <code><a rd-options="" href="/link/splitPerturbations?package=gCMAP&version=1.16.0" data-mini-rdoc="gCMAP::splitPerturbations">splitPerturbations</a></code> function. The output can be used directly as sample.annotation for the <code><a rd-options="" href="/link/NChannelSet?package=gCMAP&version=1.16.0" data-mini-rdoc="gCMAP::NChannelSet">NChannelSet</a></code> function. 


annotate_eset_list: Function to complile a data frame with per-instance annotation for a list of eSet objects generated by the `splitPerturbations` function. The output can be used directly as sample.annotation for the `NChannelSet` function.

Description

Usage

Arguments

Value

See Also

Examples