PCIT: Partial Correlation Coefficient with Information Theory

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Apply Partial Correlation coefficient with Information Theory (PCIT) to a correlation matrix. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks. To reduce compute time by making use of multiple compute cores, simply run PCIT on a computer with has multiple cores and also has the Rmpi package installed. PCIT will then auto-detect the multicore environment and run in parallel mode without the need to rewrite your scripts. This makes scripts, using PCIT, portable across single core (or no Rmpi package installed) computers which will run in serial mode and multicore (with Rmpi package installed) computers which will run in parallel mode.

Author
Nathan S. Watson-Haigh
Date of publication
2015-02-16 17:39:23
Maintainer
Nathan S. Watson-Haigh <nathan.haigh@acpfg.com.au>
License
GPL-3
Version
1.5-3
URLs

View on CRAN

Man pages

clusteringCoefficient
Calculate the clustering coefficient
clusteringCoefficientPercent
Calculate the clustering coefficient as a percentage
data
Demo Data
defineTasks
Define a list of tasks for slave CPUs
getEdgeList
Converts an adjacency matrix into edge list representation
idx
Get indicies for significant edges
idxInvert
Invert linear indices from a matrix
localClusteringCoefficient
Calculate the local clustering coefficient
maxMatrixSize
Calculate the maximum correlation matrix size which PCIT can...
pcit
Apply the PCIT algorithm
pcitMemoryRequirements
Calculate the memory requirement for running PCIT
PCIT-package
Partial Correlation coefficient with Information Theory...
plotCorCoeff
Plot superimposed histograms of correlation coefficients

Files in this package

PCIT
PCIT/inst
PCIT/inst/CITATION
PCIT/src
PCIT/src/PCIT.f90
PCIT/src/cor2cytoscape.f90
PCIT/src/localCC.f90
PCIT/NAMESPACE
PCIT/demo
PCIT/demo/PCIT.R
PCIT/demo/00Index
PCIT/data
PCIT/data/PCIT.rda
PCIT/data/datalist
PCIT/R
PCIT/R/plotCorCoeff.R
PCIT/R/clusteringCoefficientPercent.R
PCIT/R/getEdgeList.R
PCIT/R/PCIT.R
PCIT/R/clusteringCoefficient.R
PCIT/R/idx.R
PCIT/R/internal.R
PCIT/R/idxInvert.R
PCIT/R/maxMatrixSize.R
PCIT/R/localClusteringCoefficient.R
PCIT/R/defineTasks.R
PCIT/R/pcitMemoryRequirement.R
PCIT/README.md
PCIT/MD5
PCIT/DESCRIPTION
PCIT/ChangeLog
PCIT/man
PCIT/man/idx.Rd
PCIT/man/PCIT-package.Rd
PCIT/man/maxMatrixSize.Rd
PCIT/man/pcit.Rd
PCIT/man/idxInvert.Rd
PCIT/man/data.Rd
PCIT/man/clusteringCoefficient.Rd
PCIT/man/defineTasks.Rd
PCIT/man/localClusteringCoefficient.Rd
PCIT/man/plotCorCoeff.Rd
PCIT/man/pcitMemoryRequirements.Rd
PCIT/man/getEdgeList.Rd
PCIT/man/clusteringCoefficientPercent.Rd