DiffCorr: Analyzing and Visualizing Differential Correlation Networks in Biological Data

A method for identifying pattern changes between 2 experimental conditions in correlation networks (e.g., gene co-expression networks), which builds on a commonly used association measure, such as Pearson's correlation coefficient. This package includes functions to calculate correlation matrices for high-dimensional dataset and to test differential correlation, which means the changes in the correlation relationship among variables (e.g., genes and metabolites) between 2 experimental conditions.

Author
Atsushi Fukushima, Kozo Nishida
Date of publication
2015-04-02 00:07:09
Maintainer
Atsushi Fukushima <atsushi.fukushima@riken.jp>
License
GPL (> 3)
Version
0.4.1

View on CRAN

Man pages

AraMetLeaves
A metabolite data set from Arabidopsis leaves by GC-TOF/MS
AraMetRoots
A metabolite data set from Arabidopsis roots by GC-TOF/MS
cluster.molecule
Hierarchical clustering of molecules
comp.2.cc.fdr
Export differential correlations between two conditions
compcorr
Compare two correlation coefficients
cor2.test
Correlation Test
cor.dist
Additional distance functions correlation distance (1-r)
DiffCorr
Differential correlations in omics datasets
generate_g
Generating graph from data matrix
get.eigen.molecule
Get eigen molecule
get.eigen.molecule.graph
Getting graph from eigengene module list
get.lfdr
Getting local false discovery rate (lfdr)
get.min.max
Get minimum and maximum
plotClusterMolecules
Plot cluster molecules
plotDiffCorrGroup
Plot DiffCorr group
scalingMethods
scalingMethods
uncent.cor2dist
Additional distance functions correlation distance...
uncent.cordist
Calculating all pairwise distances using correlation distance
write.modules
Writing modules into a text file

Files in this package

DiffCorr
DiffCorr/NAMESPACE
DiffCorr/data
DiffCorr/data/AraMetLeaves.RData
DiffCorr/data/AraMetRoots.RData
DiffCorr/R
DiffCorr/R/data.R
DiffCorr/R/DiffCorr.R
DiffCorr/README.md
DiffCorr/MD5
DiffCorr/DESCRIPTION
DiffCorr/man
DiffCorr/man/uncent.cordist.Rd
DiffCorr/man/get.eigen.molecule.graph.Rd
DiffCorr/man/AraMetRoots.Rd
DiffCorr/man/plotClusterMolecules.Rd
DiffCorr/man/AraMetLeaves.Rd
DiffCorr/man/get.lfdr.Rd
DiffCorr/man/scalingMethods.Rd
DiffCorr/man/DiffCorr.Rd
DiffCorr/man/generate_g.Rd
DiffCorr/man/plotDiffCorrGroup.Rd
DiffCorr/man/write.modules.Rd
DiffCorr/man/cluster.molecule.Rd
DiffCorr/man/compcorr.Rd
DiffCorr/man/comp.2.cc.fdr.Rd
DiffCorr/man/get.min.max.Rd
DiffCorr/man/uncent.cor2dist.Rd
DiffCorr/man/cor.dist.Rd
DiffCorr/man/get.eigen.molecule.Rd
DiffCorr/man/cor2.test.Rd