find_pc_number.yamat: Find PC number: yamat method.

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

Find PC number: yamat method.

Description

The method is based upon Capper's method (see find_pc_number.capper). It estimates the number of the maximum eigenvalue of randomized data by repeat the randomization for several times.

Usage

find_pc_number.yamat(x, eigen_values, n = 30)

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.
n	An integer scalar of randomization times. Default to 30.

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.

• raw A data.frame of maximum eigen values and PC numbers.

Note

The Capper and yamat methods gives the same number of PCs on solid tumor example.

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