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.
|Depends:||GSEABase, limma (>= 3.15.14)|
|Imports:||Biobase, BiocGenerics, methods, GSEAlm, Category, bigmemory, bigmemoryExtras (>= 1.1.2), Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi|
|Suggests:||DESeq, KEGG.db, reactome.db, RUnit, GO.db, mgsa|
|biocViews:||Bioinformatics, Microarray, Software, Pathways, Annotation|
|Collate:||'AllClasses.R' 'AllGenerics.R' 'SignedGeneSet-accessors.R' 'utility-functions.R' 'camera_score-methods.R' 'connectivity_score-methods.R' 'featureScore-methods.R' 'fisher_score-methods.R' 'geneIndex-methods.R' 'gsealm_jg_score-methods.R' 'gsealm_score-methods.R' 'incidence-methods.R' 'mgsa_score-methods.R' 'mapIdentifiers-methods.R' 'minSetSize-methods.R' 'mroast_score-methods.R' 'romer_score-methods.R' 'wilcox_score-methods.R' 'CMAPCollection-accessors.R' 'CMAPResults-accessors.R'|
|Built:||R 3.0.0; ; 2013-03-11 17:13:45 UTC; unix|
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.DESeq_nbinom Function to perform a DESeq analysis to detect differential expression between perturbation and control groups. CMAPCollection-class Class '"CMAPCollection"' CMAPResults-class Class '"CMAPResults"' GeneSet Methods for 'GeneSet' and 'GeneColorSet' KEGG2cmap Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways <URL: http://www.wikipathways.org/index.php/Download_Pathways> project. SignedGeneSet Construtor for SignedGeneSet SignedGeneSet-class Class '"SignedGeneSet"' 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. camera_score-methods Methods for Function 'camera_score' in Package 'gCMAP' center_eSet A function to to center columns of eSet channels on either their kernel density peak, their mean or their median. connectivity_score Broad CMAP gene set enrichment metrics eSetOnDisk A function to store the assayData of an eSet object as BigMatrix files on disk. eset_instances A function to subset an eSet with expression data into smaller datasets, each corresponding to a single perturbation experiment. featureScores-methods Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet fisher_score-methods Hypergeometric probability of gene set enrichment gCMAP-package Tools for Connectivity Map-like analyses gCMAPData Example 'NChannelSet' geneIndex-methods Methods for Function 'geneIndex' in Package 'gCMAP' generate_gCMAP_NChannelSet Generate a perturbation profile library from expression sets of control/treatment pairs gsealm_jg_score-methods Parametric test for testing normally distributed scores for gene set enrichment gsealm_score-methods Methods for Function 'gsealm_score' in Package 'gCMAP' induceCMAPCollection-methods Methods for Function 'induceCMAPCollection' in Package 'gCMAP' mapNmerge A function to map eSet featureNames and calculate summaries for many-to-one mapping features matrix_or_big.matrix-class Class '"matrix_or_big.matrix"' memorize Create a new NChannelSet instance by selecting specific channels and load BigMatrix assayData into memory, if present mergeCMAPs This function merged two eSets. mgsa_score-methods Model-based gene set analysis (MGSA) minSetSize GeneSetCollection length filtering mroast_score-methods Methods for Function 'mroast_score' in Package 'gCMAP' pairwise_DESeq Generate statistics associated with pairwise differential expression from RNAseq count data pairwise_compare Generate statistics associated with pairwise differential expression romer_score-methods Methods for Function 'romer_score' in Package 'gCMAP' signedRankSumTest An implementation of the Wilcox rank sum test / Mann-Whitney test that takes into account the direction / sign of gene set members and possibly the correlation between cases splitPerturbations Function to split an ExpressionSet downloaded from ArrayExpress based on the experimental factors present in the phenoData slot wilcox_score-methods Methods for Function 'wilcox_score' in Package 'gCMAP' zScores Function to calculate z-scores from p-values
Further information is available in the following vignettes:
Thomas Sandmann <email@example.com>, Richard Bourgon <firstname.lastname@example.org> and Sarah Kummerfeld <email@example.com>
Maintainer: Thomas Sandmann <firstname.lastname@example.org>
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