removeOutliers: Removes outliers in matrix containing SNP signals

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

Removes outliers in matrix containing SNP signals

Description

Removes outliers in matrix containing SNP signals by identifying outlier elements. The values of the elements that are outliers are substituted by corresponding values predicted values Yest=W*H from the current affinity (W) and copy number (H) estimates.

Usage

removeOutliers(Y, W, H, tau=10, ...)

Arguments

Y	An IxK matrix.
W	A Kx2 matrix of probe-affinity estimates.
H	A 2xI matrix of allele-specific copy-number estimates.
tau	A scalar specifying the threshold for identifying outliers.
...	Not used.

Value

Returns an IxK matrix where outliers have been "pruned". Outliers are substituted by the corresponding value of Yest.

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