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.

AuthorThomas Sandmann <sandmann.t@gmail.com>, Richard Bourgon <bourgon.richard@gene.com> and Sarah Kummerfeld <kummerfeld.sarah@gene.com>
Date of publicationNone
MaintainerThomas Sandmann <sandmann.t@gmail.com>

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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/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/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

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