boot2fuzzy {hopach} | R Documentation

## function to write MapleTree files for viewing bootstrap estimated cluster membership probabilities based on hopach clustering results

### Description

The MapleTree software (http://mapletree.sourceforge.net/) is an open source, cross-platform, visualization tool to graphically browse results of cluster analyses. The `boot2fuzzy` function takes a data matrix, plus corresponding `hopach` clustering output and bootstrap resampling output, and writes the (.cdt, .fct, and .mb) files needed to view these "fuzzy clustering" results in MapleTree.

### Usage

    boot2fuzzy(data, bootobj, hopach.genes, hopach.arrays = NULL,
    file="hopach", clust.wts = NULL, gene.wts = NULL, array.wts = NULL,
    gene.names = NULL)

### Arguments

`data` | data matrix, data frame or exprSet of gene expression measurements. Each column corresponds to an array, and each row corresponds to a gene. All values must be numeric. Missing values are ignored.
`bootobj` | output of `boothopach` or `bootmedoids` applied to the genes - a matrix of bootstrap estimated cluster membership probabilities, with a row for each row in `data` and a column for each cluster.
`hopach.genes` | output of the `hopach` function applied to genes (rows of `data`.
`hopach.arrays` | optional output of the `hopach` function applied to arrays (columns of `data`.
`file` | name for the output files (the extensions .cdt, .mb and .fct will be added).
`clust.wts` | an optional vector of numeric weights for the clusters.
`gene.wts` | an optional vector of numeric weights for the genes.
`array.wts` | an optional vector of numeric weights for the arrays.
`gene.names` | optional vector of names or annotations for the genes, which can be different from the row names of `data`

### Value

The function `boot2fuzzy` has no value. It writes three text files to the current working directory.

### Note

Thank you to Lisa Simirenko <lsimirenko@lbl.gov> for providing HOPACH views in MapleTree, and to Karen Vranizan <vranizan@uclink.berkeley.edu> for her input. The MapleTree software can be downloaded from: http://sourceforge.net/projects/mapletree/

### Author(s)

Katherine S. Pollard <kpollard@gladstone.ucsf.edu>

### References

van der Laan, M.J. and Pollard, K.S. A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap. Journal of Statistical Planning and Inference, 2003, 117, pp. 275-303.

http://www.stat.berkeley.edu/~laan/Research/Research_subpages/Papers/hopach.pdf

### See Also

`hopach`, `boothopach`, `bootmedoids`, `hopach2tree`

### Examples

    #25 variables from two groups with 3 observations per variable
    mydata<-rbind(cbind(rnorm(10,0,0.5),rnorm(10,0,0.5),rnorm(10,0,0.5)),cbind(rnorm(15,5,0.5),rnorm(15,5,0.5),rnorm(15,5,0.5)))
    dimnames(mydata)<-list(paste("Var",1:25,sep=""),paste("Exp",1:3,sep=""))
    mydist<-distancematrix(mydata,d="cosangle") #compute the distance matrix.

    #clusters and final tree
    clustresult<-hopach(mydata,dmat=mydist)

    #bootstrap resampling
    myobj<-boothopach(mydata,clustresult)

    #write MapleTree files
    boot2fuzzy(mydata,myobj,clustresult)

[Package hopach version 2.2.0 Index]