GAPanalysis {CONFESS} | R Documentation

## GAPanalysis

### Description

It perfomrs GAP analysis using different methods. It generates the cluster numbers an an indicator of outliers.

### Usage

    GAPanalysis(data, fixClusters, sigma, altFUN, k.max, B.kmeans, savePlot, seed)

### Arguments

`data` | List. A list of adjusted fluorescence signals. Typically, the output of summarizeAdjFluo().
`fixClusters` | Integer. A number that defines the number of k-mean clusters to be initially generated. If 0, the function runs GAP analysis to estimate the optimal number of clusters.
`sigma` | Integer. A value for the sigma parameter of samSPECTRAL algorithm.
`altFUN` | Character string. A user-defined method to generate the initial clusters. It can be one of kmeans, samSpec, fmeans,fmerge or fpeaks.
`k.max` | Integer. This is the maximum number of clusters that can be generated by k-means (if fixClusters = 0).
`B.kmeans` | Integer. The number of bootstrap samples for GAP analysis in altFUN = kmeans.
`savePlot` | Character string. The directory to store the plots or an option to print them on the screen.
`seed` | Integer. An optional seed number for the Random Number Generator.

### Value

A list of adjusted fluorescence signals with cluster indices and outlier indicators (the 2s in the second column of GAPgroups).

[Package CONFESS version 1.8.0 Index]