DGCA: Differential Gene Correlation Analysis
Version 1.0.1

Performs differential correlation analysis on input matrices, with multiple conditions specified by a design matrix. Contains functions to filter, process, save, visualize, and interpret differential correlations of identifier-pairs across the entire identifier space, or with respect to a particular set of identifiers (e.g., one). Also contains several functions to perform differential correlation analysis on clusters (i.e., modules) or genes. Finally, it contains functions to generate empirical p-values for the hypothesis tests and adjust them for multiple comparisons. Although the package was built with gene expression data in mind, it is applicable to other types of genomics data as well, in addition to being potentially applicable to data from other fields entirely. It is described more fully in the manuscript introducing it, freely available at .

AuthorBin Zhang [aut], Andrew McKenzie [aut, cre]
Date of publication2016-11-17 18:33:47
MaintainerAndrew McKenzie <amckenz@gmail.com>
LicenseGPL-3
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DGCA")

Getting started

README.md
Basic differential correlation analysis using DGCA

Popular man pages

corMats-class: An S4 class to store correlation matrices and associated...
darmanis: Single-cell gene expression data from different brain cell...
ddMEGENA: Integration function to use MEGENA to perform network...
DGCA: DGCA: An R package for Differential Gene Correlation Analysis
findGOTermEnrichment: Find GO enrichment for a gene vector (using GOstats).
moduleGO: Perform module GO-trait correlation
pairwiseDCor: Calculate pairwise differential correlations.
See all...

All man pages Function index File listing

Man pages

adjustPVals: Adjusts a numeric vector of p-values.
ages_darmanis: Brain sample ages vector.
bigEmpPVals: Use speed-optimized sorting to calculate p-values observed...
corMats-class: An S4 class to store correlation matrices and associated...
darmanis: Single-cell gene expression data from different brain cell...
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...
dcTopPairs: Creates a data frame for the top differentially correlated...
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...
ddplot: Create a heatmap showing the correlations in two conditions.
design_mat: Design matrix of cell type specifications of the single-cell...
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...
getDCorPerm: Get permuted groupwise correlations and pairwise differential...
getDCors: Get groupwise correlations and pairwise differential...
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...
plotCors: Plot gene pair correlations in multiple conditions.
plotGOOneGroup: Plot results from a hypergeometric enrichment test for one...
plotGOTwoGroups: Plot results from a hypergeometric enrichment test to compare...
plotModuleGO: Plot extracted results from module-based GO enrichment...
plotVals: Creates a dotplot of the overall values for an individual...
switchGenesToHGCN: Switches a gene vector to cleaned HGNC symbols.
topDCGenes: Ranks genes by their total number of differentially...

Functions

DGCA Man page
DGCA-package Man page
adjustPVals Man page Source code
ages_darmanis Man page
bigEmpPVals Man page Source code
corMats-class Man page
dCorAvg Man page Source code
dCorClass Man page Source code
dCorMats Man page Source code
dCorrs Man page Source code
darmanis Man page
dcPair-class Man page
dcTopPairs Man page Source code
ddMEGENA Man page Source code
ddcorAll Man page Source code
ddcorFindSignificant Man page Source code
ddcorGO Man page Source code
ddplot Man page Source code
design_mat Man page
extractModuleGO Man page Source code
filterGenes Man page Source code
findGOTermEnrichment Man page Source code
getCors Man page Source code
getDCorPerm Man page Source code
getDCors Man page Source code
getGroupsFromDesign Man page Source code
makeDesign Man page Source code
matCorSig Man page Source code
matCorr Man page Source code
matNSamp Man page Source code
moduleDC Man page Source code
moduleGO Man page Source code
pairwiseDCor Man page Source code
permQValue Man page Source code
plotCors Man page Source code
plotGOOneGroup Man page Source code
plotGOTwoGroups Man page Source code
plotModuleGO Man page Source code
plotVals Man page Source code
switchGenesToHGCN Man page Source code
topDCGenes Man page Source code

Files

inst
inst/doc
inst/doc/DGCA.html
inst/doc/DGCA_modules.pdf
inst/doc/DGCA_basic.html
inst/doc/DGCA.Rmd
inst/doc/DGCA_basic.R
inst/doc/DGCA_basic.Rmd
inst/doc/DGCA_modules.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-dCorAvg.R
tests/testthat/test-ddmegena.R
tests/testthat/darmanis_design_matrix.rda
tests/testthat/test-ddcor-pipeline.R
tests/testthat/test-filterGenes.R
tests/testthat/test-matCors.R
tests/testthat/darmanis_test.rda
tests/testthat/test-dCorrs.R
tests/testthat/test-getCors.R
tests/testthat/test-adjP.R
NAMESPACE
data
data/ages_darmanis.rda
data/darmanis.rda
data/design_mat.rda
R
R/ddplot.R
R/makeDesign.R
R/bigEmpPVals.R
R/dCorClass.R
R/dCor.R
R/getDCorPerm.R
R/dCorMats.R
R/topDCGenes.R
R/plotCors.R
R/ddMEGENA.R
R/matNSamp.R
R/moduleGO.R
R/matCorSig.R
R/dgca_package.R
R/adjustPVals.R
R/moduleDC.R
R/filterGenes.R
R/dCorAvg.R
R/ddcorGO.R
R/permQValue.R
R/plotGOTwoGroups.R
R/plotVals.R
R/getDCors.R
R/matCorr.R
R/pairwiseDCor.R
R/designMats.R
R/ddcorClasses.R
R/ddcorAll.R
R/dcTopPairs.R
R/getCors.R
R/plotGOOnegroup.R
vignettes
vignettes/DGCA_basic.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/matCorSig.Rd
man/plotVals.Rd
man/dCorClass.Rd
man/plotGOTwoGroups.Rd
man/design_mat.Rd
man/getDCorPerm.Rd
man/adjustPVals.Rd
man/ddcorFindSignificant.Rd
man/dCorMats.Rd
man/dCorrs.Rd
man/extractModuleGO.Rd
man/topDCGenes.Rd
man/getCors.Rd
man/makeDesign.Rd
man/ddMEGENA.Rd
man/plotGOOneGroup.Rd
man/dcTopPairs.Rd
man/darmanis.Rd
man/matNSamp.Rd
man/pairwiseDCor.Rd
man/dCorAvg.Rd
man/ddcorGO.Rd
man/matCorr.Rd
man/permQValue.Rd
man/getDCors.Rd
man/plotCors.Rd
man/findGOTermEnrichment.Rd
man/plotModuleGO.Rd
man/switchGenesToHGCN.Rd
man/dcPair-class.Rd
man/DGCA.Rd
man/bigEmpPVals.Rd
man/ddcorAll.Rd
man/moduleGO.Rd
man/moduleDC.Rd
man/getGroupsFromDesign.Rd
man/corMats-class.Rd
man/filterGenes.Rd
man/ddplot.Rd
man/ages_darmanis.Rd
DGCA documentation built on May 19, 2017, 10:17 p.m.

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