GAPanalysis: GAPanalysis

In CONFESS: Cell OrderiNg by FluorEScence Signal

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).

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.