gCMAP: Tools for Connectivity Map-like analyses

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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.

Author
Thomas Sandmann <sandmann.t@gmail.com>, Richard Bourgon <bourgon.richard@gene.com> and Sarah Kummerfeld <kummerfeld.sarah@gene.com>
Date of publication
None
Maintainer
Thomas Sandmann <sandmann.t@gmail.com>
License
Artistic-2.0
Version
1.18.0

View on Bioconductor

Man pages

annotate_eset_list
Function to complile a data frame with per-instance...
camera_score-methods
Methods for Function 'camera_score' in Package 'gCMAP'
center_eSet
A function to to center columns of eSet channels on either...
CMAPCollection-class
Class '"CMAPCollection"'
CMAPResults-class
Class '"CMAPResults"'
connectivity_score-methods
Broad CMAP gene set enrichment metrics
DESeq_nbinom
Function to perform a DESeq analysis to detect differential...
eset_instances
A function to subset an eSet with expression data into...
eSetOnDisk
A function to store the assayData of an eSet object as...
featureScores-methods
Methods to obtain scores for CMAPCollection gene sets from a...
fisher_score-methods
Hypergeometric probability of gene set enrichment
gCMAPData-dataset
Example 'NChannelSet'
gCMAP-package
Tools for Connectivity Map-like analyses
geneIndex-methods
Methods for Function 'geneIndex' in Package 'gCMAP'
generate_gCMAP_NChannelSet
Generate a perturbation profile library from expression sets...
GeneSet-methods
Methods for 'GeneSet' and 'GeneColorSet'
gsealm_jg_score-methods
Parametric test for testing normally distributed scores for...
gsealm_score-methods
Methods for Function 'gsealm_score' in Package 'gCMAP'
induceCMAPCollection-methods
Methods for Function 'induceCMAPCollection' in Package...
KEGG2cmap
Functions to generate species-specific CMAPCollections from...
mapNmerge
A function to map eSet featureNames and calculate summaries...
matrix_or_big.matrix-class
Class '"matrix_or_big.matrix"'
memorize
Create a new NChannelSet instance by selecting specific...
mergeCMAPs
This function merged two eSets.
mgsa_score-methods
Model-based gene set analysis (MGSA)
minSetSize-methods
GeneSetCollection length filtering
mroast_score-methods
Methods for Function 'mroast_score' in Package 'gCMAP'
pairwise_compare
Generate statistics associated with pairwise differential...
pairwise_DESeq
Generate statistics associated with pairwise differential...
romer_score-methods
Methods for Function 'romer_score' in Package 'gCMAP'
SignedGeneSet-class
Class '"SignedGeneSet"'
SignedGeneSet-methods
Construtor for SignedGeneSet
signedRankSumTest
An implementation of the Wilcox rank sum test / Mann-Whitney...
splitPerturbations
Function to split an ExpressionSet downloaded from...
wilcox_score-methods
Methods for Function 'wilcox_score' in Package 'gCMAP'
zScores
Function to calculate z-scores from p-values

Files in this package

gCMAP/DESCRIPTION
gCMAP/NAMESPACE
gCMAP/R
gCMAP/R/AllClasses.R
gCMAP/R/AllGenerics.R
gCMAP/R/CMAPCollection-accessors.R
gCMAP/R/CMAPResults-accessors.R
gCMAP/R/SignedGeneSet-accessors.R
gCMAP/R/camera_score-methods.R
gCMAP/R/connectivity_score-methods.R
gCMAP/R/featureScore-methods.R
gCMAP/R/fisher_score-methods.R
gCMAP/R/geneIndex-methods.R
gCMAP/R/gsealm_jg_score-methods.R
gCMAP/R/gsealm_score-methods.R
gCMAP/R/incidence-methods.R
gCMAP/R/mapIdentifiers-methods.R
gCMAP/R/mgsa_score-methods.R
gCMAP/R/minSetSize-methods.R
gCMAP/R/mroast_score-methods.R
gCMAP/R/romer_score-methods.R
gCMAP/R/utility-functions.R
gCMAP/R/wilcox_score-methods.R
gCMAP/build
gCMAP/build/vignette.rds
gCMAP/data
gCMAP/data/gCMAPData.RData
gCMAP/inst
gCMAP/inst/NEWS.Rd
gCMAP/inst/doc
gCMAP/inst/doc/diffExprAnalysis.R
gCMAP/inst/doc/diffExprAnalysis.Rnw
gCMAP/inst/doc/diffExprAnalysis.pdf
gCMAP/inst/doc/gCMAP.R
gCMAP/inst/doc/gCMAP.Rnw
gCMAP/inst/doc/gCMAP.pdf
gCMAP/inst/unitTests
gCMAP/inst/unitTests/test_all.R
gCMAP/man
gCMAP/man/CMAPCollection-class.Rd
gCMAP/man/CMAPResults-class.Rd
gCMAP/man/DESeq_nbinom.Rd
gCMAP/man/GeneSet-methods.Rd
gCMAP/man/KEGG2cmap.Rd
gCMAP/man/SignedGeneSet-class.Rd
gCMAP/man/SignedGeneSet-methods.Rd
gCMAP/man/annotate_eset_list.Rd
gCMAP/man/camera_score-methods.Rd
gCMAP/man/center_eSet.Rd
gCMAP/man/connectivity_score-methods.Rd
gCMAP/man/eSetOnDisk.Rd
gCMAP/man/eset_instances.Rd
gCMAP/man/featureScores-methods.Rd
gCMAP/man/fisher_score-methods.Rd
gCMAP/man/gCMAP-package.Rd
gCMAP/man/gCMAPData-dataset.Rd
gCMAP/man/geneIndex-methods.Rd
gCMAP/man/generate_gCMAP_NChannelSet.Rd
gCMAP/man/gsealm_jg_score-methods.Rd
gCMAP/man/gsealm_score-methods.Rd
gCMAP/man/induceCMAPCollection-methods.Rd
gCMAP/man/mapNmerge.Rd
gCMAP/man/matrix_or_big.matrix-class.Rd
gCMAP/man/memorize.Rd
gCMAP/man/mergeCMAPs.Rd
gCMAP/man/mgsa_score-methods.Rd
gCMAP/man/minSetSize-methods.Rd
gCMAP/man/mroast_score-methods.Rd
gCMAP/man/pairwise_DESeq.Rd
gCMAP/man/pairwise_compare.Rd
gCMAP/man/romer_score-methods.Rd
gCMAP/man/signedRankSumTest.Rd
gCMAP/man/splitPerturbations.Rd
gCMAP/man/wilcox_score-methods.Rd
gCMAP/man/zScores.Rd
gCMAP/tests
gCMAP/tests/runTests.R
gCMAP/vignettes
gCMAP/vignettes/diffExprAnalysis.Rnw
gCMAP/vignettes/gCMAP.Rnw