pwod: Probe-Wise Outlier Detection

In wateRmelon: Illumina 450 methylation array normalization and metrics

Description

'P'robe-'W'ise 'O'utlier 'D'etection via interquartile ranges.

Usage

pwod(object, mul=4)

Arguments

object	MethyLumiSet, RGChannelSet, MethylSet object or matrix containing betas.
mul	Number of interquartile ranges used to determine outlying probes. Default is 4 to ensure only very obvious outliers are removed.

Details

Detects outlying probes across arrays in methylumi and minfi objects. Outliers are probable low MAF/SNP heterozygotes.

Value

Returns supplied beta matrix with outlying probes coerced to NA

Author(s)

Tyler Gorrie-Stone - [e-mail]

Examples

library(wateRmelon)
data(melon)
cattle <- betas(melon)
new.betas <- pwod(cattle, mul=4)

wateRmelon documentation built on Nov. 8, 2020, 7:47 p.m.