gCMAP: Tools for Connectivity Map-like analyses

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gCMAP")
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
Version1.18.0

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

Functions

annotate_eset_list Man page
camera_score Man page
camera_score,eSet,CMAPCollection-method Man page
camera_score,eSet,GeneSetCollection-method Man page
camera_score,eSet,GeneSet-method Man page
camera_score,matrix,CMAPCollection-method Man page
camera_score,matrix,GeneSetCollection-method Man page
camera_score,matrix,GeneSet-method Man page
camera_score-methods Man page
center_eSet Man page
CMAPCollection Man page
CMAPCollection-class Man page
CMAPCollection,environment-method Man page
CMAPCollection,matrix-method Man page
CMAPCollection,Matrix-method Man page
CMAPCollection,missing-method Man page
CMAPResults Man page
CMAPResults-class Man page
cmapTable Man page
cmapTable,CMAPResults-method Man page
connectivity_score Man page
connectivity_score,ANY,GeneSet-method Man page
connectivity_score,eSet,CMAPCollection-method Man page
connectivity_score,eSet,GeneSetCollection-method Man page
connectivity_score,eSet,SignedGeneSet-method Man page
connectivity_score,matrix,CMAPCollection-method Man page
connectivity_score,matrix,GeneSetCollection-method Man page
connectivity_score,matrix,SignedGeneSet-method Man page
.DESeq_nbinom Man page
docs Man page
docs<- Man page
docs<-,CMAPResults-method Man page
docs,CMAPResults-method Man page
downIds Man page
downIds,CMAPCollection-method Man page
downIds,SignedGeneSet-method Man page
effect Man page
effect<- Man page
effect<-,CMAPResults-method Man page
effect,CMAPResults-method Man page
errors Man page
errors<- Man page
errors<-,CMAPResults-method Man page
errors,CMAPResults-method Man page
eset_instances Man page
eSetOnDisk Man page
featureScores Man page
featureScores,BigMatrix,CMAPCollection-method Man page
featureScores,CMAPCollection,BigMatrix-method Man page
featureScores,CMAPCollection,CMAPCollection-method Man page
featureScores,CMAPCollection,eSet-method Man page
featureScores,CMAPCollection,matrix-method Man page
featureScores,CMAPCollection,matrix_or_big.matrix-method Man page
featureScores,CMAPCollection,numeric-method Man page
featureScores,eSet,CMAPCollection-method Man page
featureScores,matrix,CMAPCollection-method Man page
featureScores,matrix_or_big.matrix,CMAPCollection-method Man page
featureScores-methods Man page
featureScores,numeric,CMAPCollection-method Man page
fisher_score Man page
fisher_score,CMAPCollection,CMAPCollection,character-method Man page
fisher_score,CMAPCollection,GeneSetCollection,character-method Man page
fisher_score,CMAPCollection,NChannelSet,character-method Man page
fisher_score,GeneSet,CMAPCollection,character-method Man page
fisher_score,GeneSetCollection,CMAPCollection,character-method Man page
fisher_score,GeneSetCollection,GeneSetCollection,character-metho Man page
fisher_score,GeneSetCollection,NChannelSet,character-method Man page
fisher_score,GeneSet,GeneSet,character-method Man page
fisher_score,GeneSet,GeneSetCollection,character-method Man page
fisher_score,GeneSet,NChannelSet,character-method Man page
fisher_score-methods Man page
fisher_score,SignedGeneSet,CMAPCollection,character-method Man page
fisher_score,SignedGeneSet,NChannelSet,character-method Man page
gCMAP Man page
gCMAPData Man page
gCMAP-package Man page
GeneColorSet,NChannelSet-method Man page
geneIds,CMAPCollection-method Man page
geneIndex Man page
geneIndex,CMAPCollection,character-method Man page
geneIndex,GeneSet,character-method Man page
geneIndex,GeneSetCollection,character-method Man page
geneIndex-methods Man page
generate_gCMAP_NChannelSet Man page
geneScores Man page
geneScores,CMAPResults-method Man page
GeneSet Man page
GeneSet,NChannelSet-method Man page
geneSign Man page
geneSign<- Man page
geneSign<-,SignedGeneSet,character-method Man page
geneSign<-,SignedGeneSet,factor-method Man page
geneSign,SignedGeneSet-method Man page
go2cmap Man page
gsealm_jg_score Man page
gsealm_jg_score,CMAPCollection,eSet-method Man page
gsealm_jg_score,CMAPCollection,matrix-method Man page
gsealm_jg_score,CMAPCollection,numeric-method Man page
gsealm_jg_score,eSet,CMAPCollection-method Man page
gsealm_jg_score,eSet,GeneSetCollection-method Man page
gsealm_jg_score,eSet,GeneSet-method Man page
gsealm_jg_score,GeneSetCollection,eSet-method Man page
gsealm_jg_score,GeneSetCollection,matrix-method Man page
gsealm_jg_score,GeneSetCollection,numeric-method Man page
gsealm_jg_score,GeneSet,eSet-method Man page
gsealm_jg_score,GeneSet,matrix-method Man page
gsealm_jg_score,GeneSet,numeric-method Man page
gsealm_jg_score,matrix,GeneSetCollection-method Man page
gsealm_jg_score,matrix,GeneSet-method Man page
gsealm_jg_score,matrix_or_big.matrix,CMAPCollection-method Man page
gsealm_jg_score-methods Man page
gsealm_jg_score,numeric,CMAPCollection-method Man page
gsealm_jg_score,numeric,GeneSetCollection-method Man page
gsealm_jg_score,numeric,GeneSet-method Man page
gsealm_score Man page
gsealm_score,eSet,CMAPCollection-method Man page
gsealm_score,eSet,GeneSetCollection-method Man page
gsealm_score,eSet,GeneSet-method Man page
gsealm_score,ExpressionSet,CMAPCollection-method Man page
gsealm_score,ExpressionSet,GeneSetCollection-method Man page
gsealm_score,ExpressionSet,GeneSet-method Man page
gsealm_score,matrix,CMAPCollection-method Man page
gsealm_score,matrix,GeneSetCollection-method Man page
gsealm_score,matrix,GeneSet-method Man page
gsealm_score-methods Man page
incidence,CMAPCollection-method Man page
incidence,GeneSetCollection-method Man page
incidence,list-method Man page
incidence,SignedGeneSet-method Man page
induceCMAPCollection Man page
induceCMAPCollection,eSet-method Man page
induceCMAPCollection,matrix-method Man page
induceCMAPCollection-methods Man page
initialize,CMAPCollection-method Man page
initialize,CMAPResults-method Man page
initialize,SignedGeneSet-method Man page
KEGG2cmap Man page
ks Man page
labels Man page
labels<- Man page
labels<-,CMAPResults-method Man page
labels,CMAPResults-method Man page
mapIdentifiers,SignedGeneSet,GeneIdentifierType,GeneIdentifierTy Man page
mapIdentifiers,SignedGeneSet,GeneIdentifierType,missing-method Man page
mapIdentifiers,SignedGeneSet,missing,ANY-method Man page
mapNmerge Man page
matrix_or_big.matrix-class Man page
members Man page
members,CMAPCollection-method Man page
memorize Man page
mergeCMAPs Man page
mergeCollections Man page
mergeCollections,CMAPCollection,CMAPCollection-method Man page
mgsa_score Man page
mgsa_score,CMAPCollection,CMAPCollection,character-method Man page
mgsa_score,CMAPCollection,GeneSetCollection,character-method Man page
mgsa_score,GeneSet,CMAPCollection,character-method Man page
mgsa_score,GeneSetCollection,CMAPCollection,character-method Man page
mgsa_score,GeneSetCollection,GeneSetCollection,character-method Man page
mgsa_score,GeneSetCollection,NChannelSet,character-method Man page
mgsa_score,GeneSet,GeneSet,character-method Man page
mgsa_score,GeneSet,GeneSetCollection,character-method Man page
mgsa_score,GeneSet,NChannelSet,character-method Man page
mgsa_score-methods Man page
mgsa_score,SignedGeneSet,CMAPCollection,character-method Man page
mgsa_score,SignedGeneSet,NChannelSet,character-method Man page
minSetSize Man page
minSetSize,CMAPCollection-method Man page
mroast_score Man page
mroast_score,eSet,CMAPCollection-method Man page
mroast_score,eSet,GeneSetCollection-method Man page
mroast_score,eSet,GeneSet-method Man page
mroast_score,matrix,CMAPCollection-method Man page
mroast_score,matrix,GeneSetCollection-method Man page
mroast_score,matrix,GeneSet-method Man page
mroast_score-methods Man page
nFound Man page
nFound<- Man page
nFound<-,CMAPResults-method Man page
nFound,CMAPResults-method Man page
nSet Man page
nSet<- Man page
nSet<-,CMAPResults-method Man page
nSet,CMAPResults-method Man page
padj Man page
padj<- Man page
padj<-,CMAPResults-method Man page
padj,CMAPResults-method Man page
pairwise_compare Man page
pairwise_compare_limma Man page
pairwise_DESeq Man page
plot,CMAPResults,ANY-method Man page
pval Man page
pval<- Man page
pval<-,CMAPResults-method Man page
pval,CMAPResults-method Man page
reactome2cmap Man page
romer_score Man page
romer_score,eSet,CMAPCollection-method Man page
romer_score,eSet,GeneSetCollection-method Man page
romer_score,eSet,GeneSet-method Man page
romer_score,matrix,CMAPCollection-method Man page
romer_score,matrix,GeneSetCollection-method Man page
romer_score,matrix,GeneSet-method Man page
romer_score-methods Man page
s Man page
S Man page
set Man page
set<- Man page
set<-,CMAPResults-method Man page
set,CMAPResults-method Man page
setSizes Man page
setSizes,CMAPCollection-method Man page
show,CMAPResults-method Man page
show,SignedGeneSet-method Man page
signed Man page
signed<- Man page
signed<-,CMAPCollection-method Man page
signed,CMAPCollection-method Man page
SignedGeneSet Man page
SignedGeneSet,ANY-method Man page
SignedGeneSet-class Man page
SignedGeneSet,missing-method Man page
signedRankSumTest Man page
splitPerturbations Man page
trend Man page
trend<- Man page
trend<-,CMAPResults-method Man page
trend,CMAPResults-method Man page
upIds Man page
upIds,CMAPCollection-method Man page
upIds,SignedGeneSet-method Man page
wiki2cmap Man page
wilcox_score Man page
wilcox_score,CMAPCollection,eSet-method Man page
wilcox_score,CMAPCollection,matrix-method Man page
wilcox_score,CMAPCollection,numeric-method Man page
wilcox_score,eSet,CMAPCollection-method Man page
wilcox_score,eSet,GeneSetCollection-method Man page
wilcox_score,eSet,GeneSet-method Man page
wilcox_score,GeneSetCollection,eSet-method Man page
wilcox_score,GeneSetCollection,matrix-method Man page
wilcox_score,GeneSetCollection,numeric-method Man page
wilcox_score,GeneSet,eSet-method Man page
wilcox_score,GeneSet,matrix-method Man page
wilcox_score,GeneSet,numeric-method Man page
wilcox_score,matrix,CMAPCollection-method Man page
wilcox_score,matrix,GeneSetCollection-method Man page
wilcox_score,matrix,GeneSet-method Man page
wilcox_score-methods Man page
wilcox_score,numeric,CMAPCollection-method Man page
wilcox_score,numeric,GeneSetCollection-method Man page
wilcox_score,numeric,GeneSet-method Man page
zscores Man page
zScores Man page
zscores,CMAPResults-method Man page

Files

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/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

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