WHInit: Initialization of the W and H matrices

In HenrikBengtsson/ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

Initialization of the W and H matrices

Description

Initialization of the W and H matrices.

Usage

WHInit(V, ...)

Arguments

V	An KxI matrix where I is the number of arrays and K is the number of probes where K should be even (K=2L).
...	Not used.

Details

The allele-specific copy number estimates are estimated using a naive genotyping algorithm. The probe-affinities are estimated using a pseudo inverse.

Value

Returns a list:

W	A Kx2 matrix of initial probe-affinity estimates.
H	A 2xI matrix of initial allele-specific copy-number estimates.
status	An integer specifying the status of the initialization: 0=normal case, 1=only one allele (either AA or BB), or 2=all samples are AB.

HenrikBengtsson/ACNE documentation built on Feb. 20, 2024, 8:20 p.m.