find_pc_number.capper: Find PC number: Capper's method.

In markgene/yamatClassifier: Yet Another Methylation Array Toolkit: Classifier

Find PC number: Capper's method.

Description

The method is described in the paper by Capper et al. entitled "DNA methylation-based classification of central nervous system tumours". In brief, the method shuffles features across samples and determine the PC number by comparing the maximum of eigen values from the randomization.

Usage

find_pc_number.capper(x, eigen_values)

Arguments

x	A matrix which has columns as features and rows as samples.
eigen_values	A vector of eigen values. It is the item values of the item eigs of the returned value of pca123, which is returned by eigs.

Value

A list of three items:

• pc_num An integer scalar of PC number.

• variance_fraction The sum of fraction of variance of pc_num PCs.

• eigs_shuffled A numeric vector of eigen values of the randomized data.

• plot A ggplot object of density plot of eigenvalues of observed and randomized data.

markgene/yamatClassifier documentation built on Oct. 14, 2024, 2:36 a.m.