GAPanalysis {CONFESS} | R Documentation |
It perfomrs GAP analysis using different methods. It generates the cluster numbers an an indicator of outliers.
GAPanalysis(data, fixClusters, sigma, altFUN, k.max, B.kmeans, savePlot, seed)
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. |
A list of adjusted fluorescence signals with cluster indices and outlier indicators (the 2s in the second column of GAPgroups).