Differential Gene Correlation Analysis

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Documentation for package ‘DGCA’ version 1.0.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

DGCA-package	DGCA: An R package for Differential Gene Correlation Analysis
adjustPVals	Adjusts a numeric vector of p-values.
ages_darmanis	Brain sample ages vector.
bigEmpPVals	Use speed-optimized sorting to calculate p-values observed and simulated null test statistic using a reference pool distribution.
corMats-class	An S4 class to store correlation matrices and associated info.
darmanis	Single-cell gene expression data from different brain cell types.
dCorAvg	Get average empirical differential correlations.
dCorClass	Classify differential correlations.
dCorMats	Finds differential correlations between matrices.
dCorrs	Differential correlation between two conditions.
dcPair-class	S4 class for pairwise differential correlation matrices and associated info.
dcTopPairs	Creates a data frame for the top differentially correlated gene pairs in your data set.
ddcorAll	Calls the DGCA pairwise pipeline.
ddcorFindSignificant	Find groups of differentially correlated gene symbols.
ddcorGO	Gene ontology of differential correlation-classified genes.
ddMEGENA	Integration function to use MEGENA to perform network analyses of DGCA results.
ddplot	Create a heatmap showing the correlations in two conditions.
design_mat	Design matrix of cell type specifications of the single-cell RNA-seq samples.
DGCA	DGCA: An R package for Differential Gene Correlation Analysis
extractModuleGO	Extract results from the module GO analysis
filterGenes	Filter rows out of a matrix.
findGOTermEnrichment	Find GO enrichment for a gene vector (using GOstats).
getCors	Compute matrices necessary for differential correlation calculation.
getDCorPerm	Get permuted groupwise correlations and pairwise differential correlations.
getDCors	Get groupwise correlations and pairwise differential correlations.
getGroupsFromDesign	Split input matrix(es) based on the design matrix.
makeDesign	Create a design matrix from a character vector.
matCorr	Calculate a correlation matrix.
matCorSig	Calculate correlation matrix p-values.
matNSamp	Find the number of non-missing values.
moduleDC	Calculate modular differential connectivity (MDC)
moduleGO	Perform module GO-trait correlation
pairwiseDCor	Calculate pairwise differential correlations.
permQValue	Calculate q-values from DGCA class objects based on permutation-based empirical null statistics.
plotCors	Plot gene pair correlations in multiple conditions.
plotGOOneGroup	Plot results from a hypergeometric enrichment test for one condition.
plotGOTwoGroups	Plot results from a hypergeometric enrichment test to compare two conditions.
plotModuleGO	Plot extracted results from module-based GO enrichment analysis using ggplot2.
plotVals	Creates a dotplot of the overall values for an individual gene in multiple conditions.
switchGenesToHGCN	Switches a gene vector to cleaned HGNC symbols.
topDCGenes	Ranks genes by their total number of differentially correlated gene pairs.