gimmRFromPos: Method to create gimmR object corresponding to .pos file.

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

Description

This method first creates the table object from .pos file, and then uses this object as input to runGimmNPosthoc(). Before running this method, user must run either runGimm() and runPosthoc() or runGimmNPosthoc(), so that .pos file is generated.

Usage

gimmRFromPos(posDataFileName, M, T, nIter=10000, nreplicates=1,
				 contextSpecific="n", nContexts=1, contextLengths=NA,
				 clusterShape="v", burnIn=5000, elipticalWithin="n", matrixOut="n",
				 readingRaw="y", probsOut="y", clusterNumber=2,
				 clusterOption="average", verbose=FALSE, intFiles=FALSE)

Arguments

posDataFileName	Name of the .pos file. if not provided, default fileName is taken as "Result.pos". If file not found, method throws an error.
M	Dimensionality of the expression vectors to be clustered. I.e. the number of microarray. Same as given to runGimmNPosthoc() before running this method.
T	Number of genes to be clustered. Same as given to runGimmNPosthoc() before running this method.
nIter	Number of iterations to be generated by the Gibbs sampler. Same as given to runGimmNPosthoc() before running this method.
nreplicates	Number of experimental replicates. Same as given to runGimmNPosthoc() before running this method.
contextSpecific	This parameter specifies whether the context-specific model to be used. If set to "y", the nContexts and contextLengths need also to be specified.
nContexts	Number of contexts to be used in the context-specific clustering. If nContexts>1 is specified, the context-specific model is assumed.
contextLengths	Vector specifying lengths of the contexts in the context-specific clustering. It has to satisfy following equality sum(contextLenghts)==M
clusterShape	"v" requests the model with different variances for different clusters. "e" assumes equal variances for all clusters.
burnIn	Number of Gibbs sampler iterations to be discarded as "burn-in".
elipticalWithin	This parameter indicates the structure of covariance matrix in model. The covariance matrix defines the correlation of observations from different experimental conditions. For experimental design model, its value is "d", for compound symmetry model, its value is "c" while for unstructured model; its value is "n".
matrixOut	Not used
readingRaw	Not used
probsOut	Not used
clusterNumber	Not used
clusterOption	Linkage principle to be used in constructing hierarchical clustering. "average" and "complete" are supported.
verbose	If true, all the internal cmments of the executables will be displayed on console.
intFiles	If true, the internal files generated by the executables gimm and posthoc won't be deleted.

Note

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

Author(s)

Vinayak Kumar, Mario Medvedovic

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