DGCA: Differential Gene Correlation Analysis

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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 <doi:10.1186/s12918-016-0349-1>.

Author
Bin Zhang [aut], Andrew McKenzie [aut, cre]
Date of publication
2016-11-17 18:33:47
Maintainer
Andrew McKenzie <amckenz@gmail.com>
License
GPL-3
Version
1.0.1

View on CRAN

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...

Files in this package

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