gCMAP: Tools for Connectivity Map-like analyses
Version 1.20.0

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.

AuthorThomas Sandmann <sandmann.t@gmail.com>, Richard Bourgon <bourgon.richard@gene.com> and Sarah Kummerfeld <kummerfeld.sarah@gene.com>
Bioconductor views Annotation Microarray Pathways Software
Date of publicationNone
MaintainerThomas Sandmann <sandmann.t@gmail.com>
LicenseArtistic-2.0
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gCMAP")

Getting started

Package overview

Popular man pages

camera_score-methods: Methods for Function 'camera_score' in Package 'gCMAP'
CMAPCollection-class: Class '"CMAPCollection"'
connectivity_score-methods: Broad CMAP gene set enrichment metrics
eset_instances: A function to subset an eSet with expression data into...
gCMAP-package: Tools for Connectivity Map-like analyses
wilcox_score-methods: Methods for Function 'wilcox_score' in Package 'gCMAP'
zScores: Function to calculate z-scores from p-values
See all...

All man pages Function index File listing

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

Functions

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/CMAPCollection-accessors.R
R/CMAPResults-accessors.R
R/SignedGeneSet-accessors.R
R/camera_score-methods.R
R/connectivity_score-methods.R
R/featureScore-methods.R
R/fisher_score-methods.R
R/geneIndex-methods.R
R/gsealm_jg_score-methods.R
R/gsealm_score-methods.R
R/incidence-methods.R
R/mapIdentifiers-methods.R
R/mgsa_score-methods.R
R/minSetSize-methods.R
R/mroast_score-methods.R
R/romer_score-methods.R
R/utility-functions.R
R/wilcox_score-methods.R
build
build/vignette.rds
data
data/gCMAPData.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/diffExprAnalysis.R
inst/doc/diffExprAnalysis.Rnw
inst/doc/diffExprAnalysis.pdf
inst/doc/gCMAP.R
inst/doc/gCMAP.Rnw
inst/doc/gCMAP.pdf
inst/unitTests
inst/unitTests/test_all.R
man
man/CMAPCollection-class.Rd
man/CMAPResults-class.Rd
man/DESeq_nbinom.Rd
man/GeneSet-methods.Rd
man/KEGG2cmap.Rd
man/SignedGeneSet-class.Rd
man/SignedGeneSet-methods.Rd
man/annotate_eset_list.Rd
man/camera_score-methods.Rd
man/center_eSet.Rd
man/connectivity_score-methods.Rd
man/eSetOnDisk.Rd
man/eset_instances.Rd
man/featureScores-methods.Rd
man/fisher_score-methods.Rd
man/gCMAP-package.Rd
man/gCMAPData-dataset.Rd
man/geneIndex-methods.Rd
man/generate_gCMAP_NChannelSet.Rd
man/gsealm_jg_score-methods.Rd
man/gsealm_score-methods.Rd
man/induceCMAPCollection-methods.Rd
man/mapNmerge.Rd
man/matrix_or_big.matrix-class.Rd
man/memorize.Rd
man/mergeCMAPs.Rd
man/mgsa_score-methods.Rd
man/minSetSize-methods.Rd
man/mroast_score-methods.Rd
man/pairwise_DESeq.Rd
man/pairwise_compare.Rd
man/romer_score-methods.Rd
man/signedRankSumTest.Rd
man/splitPerturbations.Rd
man/wilcox_score-methods.Rd
man/zScores.Rd
tests
tests/runTests.R
vignettes
vignettes/diffExprAnalysis.Rnw
vignettes/gCMAP.Rnw
gCMAP documentation built on May 20, 2017, 10:21 p.m.

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