gapStat: gapStat

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Description

Based on dissmilarity measurement, we define Wk = sum(sum(d_ij)/2n_r)

Usage

gapStat(data = NULL, dendro = NULL, dendref = NULL, cmax = 0.24,
  cmin = 0.04, mcore = 2, log = FALSE, verbose = TRUE, ...)

Arguments

data	methylation data matrix
dendro	actual dendrogram
dendref	reference dendrogram
cmax	maximum dissimilarity Default 0.22
cmin	minimun dissimilarity Default 0.02
mcore	number of threads running
log	FALSE(Default). Standardize by log or not
verbose	verbose
...	optional parameters for distributeRef and HClust

Details

grid search for CLuster number detection by gap statistic

Value

list of clusterDetect labels number Wk within sum of dissimilarity EWk expectation of Wk under null reference distribution

Author(s)

Xin Zhou [e-mail]

xinchoubiology/Rcppsva documentation built on May 4, 2019, 1:06 p.m.