# Differential Gene Correlation Analysis

## Documentation for package ‘DGCA’ version 1.0.1

- 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.