runPosthoc: This function prepares parameters for running executable...

In uc-bd2k/gimmR: This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.

Description

Function to complete all the processes related to "posthoc". By calling this function, all the operations regarding posthoc can be performed, but all the other processes related to gimm are not be executed.

User must provide the list data of all the parameters required for "posthoc" execution. This list will be available as the result of function "runGimm".

Usage

runPosthoc (commonParamsNData, matrixOut="n", readingRaw="y",
            probsOut="y", clusterNumber=2, clusterOption="average", 
			estimate_contexts="n", clientID=-1, host=-1, port=-1)

Arguments

commonParamsNData	List data of parameters and data. Some of the parameters in this list will be used in this function. This list is the result produced by function "runGimm".
matrixOut	Not used
readingRaw	Not used
probsOut	Not used
clusterNumber	Number of clusters created by cutting the hierarchical clustering tree
clusterOption	Linkage principle to be used in constructing hierarchical clustering. "average" and "complete" are supported.
estimate_contexts	"y" the context estimation GIMM was run. "n" the fixed contexts model or simple GIMM was run.
clientID	The clientID that identifies the specific client to which the progress feedbacks are directed. This should be used only if feedback about progress need to be sent over network sockets.
host	The hostname for the computer to which progress feedbacks should be sent. This should be used only if feedback about progress need to be sent over network sockets.
port	The port number to which progress feedbacks should be sent. This should be used only if feedback about progress need to be sent over network sockets.

Details

This function is designed to execute the processes related to "posthoc" only. It makes call to function "processPosthocParas()" using which parameter file called "posthoc\_parameters.prm" are written. Then system call is made to executable "posthoc". User is supposed to provide the directory path in which these executables are residing. This can be done by changing the objects ".PosthocPath" in the library.

In order to complete all the processings for Bayesian Clusttering algorithm, call to this function should be preceded by call to function "runGimm".

This function provides the result via the .cdt and .gtr files.

Note

For additional information visit http://eh3.uc.edu/gimm

Author(s)

Vinayak Kumar, Mario Medvedovic

See Also

runGimm

uc-bd2k/gimmR documentation built on May 3, 2019, 2:15 p.m.