# Tools for Connectivity Map-like analyses

## Documentation for package ‘gCMAP’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G I K L M N P R S T U W Z misc

gCMAP-package | Tools for Connectivity Map-like analyses

## -- A --

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.

## -- C --

camera_score | Methods for Function 'camera_score' in Package 'gCMAP'
camera_score-method | Methods for Function 'camera_score' in Package 'gCMAP'
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.
CMAPCollection | Class '"CMAPCollection"'
CMAPCollection-class | Class '"CMAPCollection"'
CMAPCollection-method | Class '"CMAPCollection"'
CMAPResults | Class '"CMAPResults"'
CMAPResults-class | Class '"CMAPResults"'
cmapTable | Class '"CMAPResults"'
cmapTable-method | Class '"CMAPResults"'
connectivity_score | Broad CMAP gene set enrichment metrics
connectivity_score-method | Broad CMAP gene set enrichment metrics

## -- D --

docs | Class '"CMAPResults"'
docs-method | Class '"CMAPResults"'
docs<- | Class '"CMAPResults"'
docs<--method | Class '"CMAPResults"'
downIds | Class '"SignedGeneSet"'
downIds-method | Class '"CMAPCollection"'
downIds-method | Class '"SignedGeneSet"'

## -- E --

effect | Class '"CMAPResults"'
effect-method | Class '"CMAPResults"'
effect<- | Class '"CMAPResults"'
effect<--method | Class '"CMAPResults"'
errors | Class '"CMAPResults"'
errors-method | Class '"CMAPResults"'
errors<- | Class '"CMAPResults"'
errors<--method | Class '"CMAPResults"'
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.

## -- F --

featureScores | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet
featureScores-method | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet
featureScores-methods | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet
fisher_score | Hypergeometric probability of gene set enrichment
fisher_score-method | Hypergeometric probability of gene set enrichment
fisher_score-methods | Hypergeometric probability of gene set enrichment

## -- G --

gCMAP | Tools for Connectivity Map-like analyses
gCMAPData | Example 'NChannelSet'
GeneColorSet-method | Methods for 'GeneSet' and 'GeneColorSet'
geneIds-method | Class '"CMAPCollection"'
geneIndex | Methods for Function 'geneIndex' in Package 'gCMAP'
geneIndex-method | Methods for Function 'geneIndex' in Package 'gCMAP'
geneIndex-methods | Methods for Function 'geneIndex' in Package 'gCMAP'
generate_gCMAP_NChannelSet | Generate a perturbation profile library from expression sets of control/treatment pairs
geneScores | Class '"CMAPResults"'
geneScores-method | Class '"CMAPResults"'
GeneSet | Methods for 'GeneSet' and 'GeneColorSet'
GeneSet-method | Methods for 'GeneSet' and 'GeneColorSet'
geneSign | Class '"SignedGeneSet"'
geneSign-method | Class '"SignedGeneSet"'
geneSign<- | Class '"SignedGeneSet"'
geneSign<--method | Class '"SignedGeneSet"'
go2cmap | 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.
gsealm_jg_score | Parametric test for testing normally distributed scores for gene set enrichment
gsealm_jg_score-method | Parametric test for testing normally distributed scores for gene set enrichment
gsealm_jg_score-methods | Parametric test for testing normally distributed scores for gene set enrichment
gsealm_score | Methods for Function 'gsealm_score' in Package 'gCMAP'
gsealm_score-method | Methods for Function 'gsealm_score' in Package 'gCMAP'
gsealm_score-methods | Methods for Function 'gsealm_score' in Package 'gCMAP'

## -- I --

incidence-method | Class '"CMAPCollection"'
incidence-method | Class '"SignedGeneSet"'
induceCMAPCollection | Methods for Function 'induceCMAPCollection' in Package 'gCMAP'
induceCMAPCollection-method | Methods for Function 'induceCMAPCollection' in Package 'gCMAP'
induceCMAPCollection-methods | Methods for Function 'induceCMAPCollection' in Package 'gCMAP'
initialize-method | Class '"CMAPCollection"'
initialize-method | Class '"CMAPResults"'
initialize-method | Class '"SignedGeneSet"'

## -- K --

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.
ks | Broad CMAP gene set enrichment metrics

## -- L --

labels | Class '"CMAPResults"'
labels-method | Class '"CMAPResults"'
labels<- | Class '"CMAPResults"'
labels<--method | Class '"CMAPResults"'

## -- M --

mapIdentifiers-method | Class '"SignedGeneSet"'
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"'
members | Class '"CMAPCollection"'
members-method | Class '"CMAPCollection"'
memorize | Create a new NChannelSet instance by selecting specific channels and load BigMatrix assayData into memory.
mergeCMAPs | This function merged two eSets.
mergeCollections | Class '"CMAPCollection"'
mergeCollections-method | Class '"CMAPCollection"'
mgsa_score | Model-based gene set analysis (MGSA)
mgsa_score-method | Model-based gene set analysis (MGSA)
mgsa_score-methods | Model-based gene set analysis (MGSA)
minSetSize | GeneSetCollection length filtering
minSetSize-method | GeneSetCollection length filtering
mroast_score | Methods for Function 'mroast_score' in Package 'gCMAP'
mroast_score-method | Methods for Function 'mroast_score' in Package 'gCMAP'
mroast_score-methods | Methods for Function 'mroast_score' in Package 'gCMAP'

## -- N --

nFound | Class '"CMAPResults"'
nFound-method | Class '"CMAPResults"'
nFound<- | Class '"CMAPResults"'
nFound<--method | Class '"CMAPResults"'
nSet | Class '"CMAPResults"'
nSet-method | Class '"CMAPResults"'
nSet<- | Class '"CMAPResults"'
nSet<--method | Class '"CMAPResults"'

## -- P --

padj | Class '"CMAPResults"'
padj-method | Class '"CMAPResults"'
padj<- | Class '"CMAPResults"'
padj<--method | Class '"CMAPResults"'
pairwise_compare | Generate statistics associated with pairwise differential expression
pairwise_compare_limma | Generate statistics associated with pairwise differential expression
pairwise_DESeq | Generate statistics associated with pairwise differential expression from RNAseq count data
plot-method | Class '"CMAPResults"'
pval | Class '"CMAPResults"'
pval-method | Class '"CMAPResults"'
pval<- | Class '"CMAPResults"'
pval<--method | Class '"CMAPResults"'

## -- R --

reactome2cmap | 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.
romer_score | Methods for Function 'romer_score' in Package 'gCMAP'
romer_score-method | Methods for Function 'romer_score' in Package 'gCMAP'
romer_score-methods | Methods for Function 'romer_score' in Package 'gCMAP'

## -- S --

S | Broad CMAP gene set enrichment metrics
s | Broad CMAP gene set enrichment metrics
set | Class '"CMAPResults"'
set-method | Class '"CMAPResults"'
set<- | Class '"CMAPResults"'
set<--method | Class '"CMAPResults"'
setSizes | Class '"CMAPCollection"'
setSizes-method | Class '"CMAPCollection"'
show-method | Class '"CMAPResults"'
show-method | Class '"SignedGeneSet"'
signed | Class '"CMAPCollection"'
signed-method | Class '"CMAPCollection"'
signed<- | Class '"CMAPCollection"'
signed<--method | Class '"CMAPCollection"'
SignedGeneSet | Construtor for SignedGeneSet
SignedGeneSet-class | Class '"SignedGeneSet"'
SignedGeneSet-method | Construtor for SignedGeneSet
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

## -- T --

trend | Class '"CMAPResults"'
trend-method | Class '"CMAPResults"'
trend<- | Class '"CMAPResults"'
trend<--method | Class '"CMAPResults"'

## -- U --

upIds | Class '"SignedGeneSet"'
upIds-method | Class '"CMAPCollection"'
upIds-method | Class '"SignedGeneSet"'

## -- W --

wiki2cmap | 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.
wilcox_score | Methods for Function 'wilcox_score' in Package 'gCMAP'
wilcox_score-method | Methods for Function 'wilcox_score' in Package 'gCMAP'
wilcox_score-methods | Methods for Function 'wilcox_score' in Package 'gCMAP'

## -- Z --

zScores | Function to calculate z-scores from p-values
zscores | Class '"CMAPResults"'
zscores-method | Class '"CMAPResults"'

## -- misc --

.DESeq_nbinom | Function to perform a DESeq analysis to detect differential expression between perturbation and control groups.