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.