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 |

http://dx.doi.org/10.1093/bioinformatics/btn482 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/3/411 |

**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

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
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