GuidedSparseKmeans.KLam.R2out: GuidedSparseKmeans.KLam.R2out

Description Usage Arguments Details Value Author(s)

View source: R/GuidedSparseKmeans.KLam.R2out.R

Description

Selection of Tuning Parameter K and lam in Guided Sparse K-means (R-square or pseudo R-square is from the outside)

Usage

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GuidedSparseKmeans.KLam.R2out(x, R2.per, pre.K = NULL, s.one,
  nstart = 20, maxiter = 15, silence = F)

Arguments

x

Gene expression matrix, n*p (rows for subjects and columns for genes).

R2.per

R-squared or pseudo R-squared between phenotypic variable and expression value of each gene, a vector.

pre.K

Pre-knowledge of the number of clusters.

s.one

A proper value of the boundary of l1n weights.

nstart

Specify the number of starting point for K-means.

maxiter

Maximum number of iteration.

silence

Output progress or not.

Details

Select tuning parameter K using gap statistics and tuning parameter lam using sensitivity analysis in Guided Sparse K-means integrating clinical dataset with gene expression dataset, R-square or pseudo R-square is from the outside, not calculated in the function.

Value

A list consisting of

K.select

value of selected K.

lam.select

value of selected lam.

ARI.Cs

Adjusted ARI values for cluster results.

Jaccard.gene

Jaccard index values for gene selection results.

Author(s)

Lingsong Meng


LingsongMeng/GuidedSparseKmeans documentation built on May 11, 2020, 12:29 a.m.