meffil.handle.outliers: Handle outliers in a methylation matrix

In perishky/meffil: Efficient algorithms for DNA methylation

Handle outliers in a methylation matrix

Description

Handle outliers in a methylation matrix

Usage

meffil.handle.outliers(beta, winsorize.pct = 0.05, outlier.iqr.factor = NA)

Arguments

beta	Methylation matrix (rows=CpG sites, columns=samples, values=methylation levels).
winsorize.pct	Apply all regression models to methylation levels winsorized to the given level. Set to NA to avoid winsorizing (Default: 0.05).
outlier.iqr.factor	For each CpG site, prior to fitting regression models, set methylation levels less than Q1 - outlier.iqr.factor * IQR or more than Q3 + outlier.iqr.factor * IQR to NA. Here IQR is the inter-quartile range of the methylation levels at the CpG site, i.e. Q3-Q1. Set to NA to skip this step (Default: NA).

Value

beta after winsorizing and outliers set to NA.

perishky/meffil documentation built on June 9, 2024, 5:59 p.m.