Graphical user interface for Mfuzz package

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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

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

  1. 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.

  2. 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.

  3. Mfuzz web-page: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz

See Also

mfuzz

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