Mfuzzgui: Graphical user interface for Mfuzz package
In Mfuzz: Soft clustering of time series gene expression data
Description
Usage
Details
Value
Note
Author(s)
References
See Also
Description
The function Mfuzzgui provides a graphical user interface for
clustering of microarray data and visualisation of results.
It is based on the functions of the Mfuzz package.
Usage
1
Mfuzzgui()
Details
The function Mfuzzgui launches a graphical user interface for the Mfuzz package.
It is based on Tk widgets using the R TclTk interface by Peter Dalgaard. It also employs
some pre-made widgets from the tkWidgets Bioconductor-package by Jianhua Zhang for
the selection of objects/files to be loaded.
Mfuzzgui provides a convenient interface to most functions of the Mfuzz package without restriction
of flexibility. An exception is the batch processes such as partcoeff and cselection routines which
are used for parameter selection in fuzzy c-means clustering of microarray data. These routines are
not included in Mfuzzgui. To select various parameters, the underlying Mfuzz routines may be applied.
Usage of Mfuzzgui does not require assumes an pre-built exprSet object
but can be used with tab-delimited text files containing the gene expression data.
Note, however, that the clustering is based on the
the ordering of samples (arrays) as
of the columns in the expression matrix of the exprSet object or in the uploaded table, respectively.
Also, replicated arrays in the
expression matrix (or table) are treated as independent by the mfuzz function
and, thus, should be averagered prior to clustering.
For a overview of the functionality of Mfuzzgui, please refer to the package vignette. For a description
of the underlying functions, please refer to the Mfuzz package.
Value
Mfuzzgui returns a tclObj object.
Note
The newest versions of Mfuzzgui can be found at the Mfuzz webpage
(http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz).
Author(s)
Matthias E. Futschik
(http://itb.biologie.hu-berlin.de/~futschik)and Lokesh Kumar
References
M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics
and Computational Biology, Vol. 3, No. 4, 965-988, 2005.
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart
DJ, Davis RW, A genome-wide transcriptional analysis of the mitotic cell cycle, Mol Cell,(2):65-73, 1998.
Mfuzz web-page: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz
See Also
Mfuzz documentation built on Nov. 8, 2020, 5:22 p.m.
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Description Usage Details Value Note Author(s) References See Also
Description
The function Mfuzzgui provides a graphical user interface for
clustering of microarray data and visualisation of results.
It is based on the functions of the Mfuzz package.
Usage
1 | Mfuzzgui()
|
Details
The function Mfuzzgui launches a graphical user interface for the Mfuzz package.
It is based on Tk widgets using the R TclTk interface by Peter Dalgaard. It also employs
some pre-made widgets from the tkWidgets Bioconductor-package by Jianhua Zhang for
the selection of objects/files to be loaded.
Mfuzzgui provides a convenient interface to most functions of the Mfuzz package without restriction
of flexibility. An exception is the batch processes such as partcoeff and cselection routines which
are used for parameter selection in fuzzy c-means clustering of microarray data. These routines are
not included in Mfuzzgui. To select various parameters, the underlying Mfuzz routines may be applied.
Usage of Mfuzzgui does not require assumes an pre-built exprSet object
but can be used with tab-delimited text files containing the gene expression data.
Note, however, that the clustering is based on the
the ordering of samples (arrays) as
of the columns in the expression matrix of the exprSet object or in the uploaded table, respectively.
Also, replicated arrays in the
expression matrix (or table) are treated as independent by the mfuzz function
and, thus, should be averagered prior to clustering.
For a overview of the functionality of Mfuzzgui, please refer to the package vignette. For a description
of the underlying functions, please refer to the Mfuzz package.
Value
Mfuzzgui returns a tclObj object.
Note
The newest versions of Mfuzzgui can be found at the Mfuzz webpage
(http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz).
Author(s)
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)and Lokesh Kumar
References
M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-988, 2005.
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW, A genome-wide transcriptional analysis of the mitotic cell cycle, Mol Cell,(2):65-73, 1998.
Mfuzz web-page: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz
See Also
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