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Last data update: 2014.03.03

R: Figure of Merit

fom	R Documentation

Figure of Merit

Description

K-means clustering needs a given number of groups, which is difficult to guess in most of the cases. This function calculates the Figure of Merit values for different number of groups and generates the FOM plot (FOM value versus number of groups). Lower FOM value means better grouping. User can decide the number of groups in kmeans cluster based on that result.

Usage

fom(anovaobj, idx.gene, term, ngroups)

Arguments

`anovaobj`	An object of class `maanova`.
`idx.gene`	The index of genes to be clustered.
`term`	The factor (in formula) used in clustering. The expression level for this term will be used in clustering. This term has to correspond to the gene list, e.g, idx.gene in this function. The gene list should be the significant hits in testing this term.
`ngroups`	The number of groups for K-means cluster. This could be a vector or an integer.

Value

A vector of FOM values for the given number of groups

Author(s)

Hao Wu

References

Yeung, K.Y., D.R. Haynor, and W.L.Ruzzo (2001). Validating clustering for gene expression data. Bioinformatics, 17:309-318.

Examples

# load in data
data(abf1)
# fit the anova model
## Not run: 
fit.fix = fitmaanova(abf1,formula = ~Strain)
# test Strain effect 
test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
# pick significant genes - pick the genes selected by Fs test
idx <- volcano(test.fix)$idx.Fs
# generate FOM
m <- fom(fit.fix, idx, "Strain", 10)
## End(Not run)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(maanova)

Attaching package: 'maanova'

The following object is masked from 'package:base':

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maanova/fom.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fom
> ### Title: Figure of Merit
> ### Aliases: fom
> ### Keywords: models
> 
> ### ** Examples
> 
> # load in data
> data(abf1)
> # fit the anova model
> ## Not run: 
> ##D fit.fix = fitmaanova(abf1,formula = ~Strain)
> ##D # test Strain effect 
> ##D test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
> ##D # pick significant genes - pick the genes selected by Fs test
> ##D idx <- volcano(test.fix)$idx.Fs
> ##D # generate FOM
> ##D m <- fom(fit.fix, idx, "Strain", 10)
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>