dyeBiasNL: Dye bias correction by matching green and red to mid point
In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

dyeBiasNL

R Documentation

Dye bias correction by matching green and red to mid point

Description

This function compares the Type-I Red probes and Type-I Grn probes and generates and mapping to correct signal of the two channels to the middle. The function takes one single SigDF and returns a SigDF with dye bias corrected.

Usage

dyeBiasNL(sdf, mask = TRUE, verbose = FALSE)

dyeBiasCorrTypeINorm(sdf, mask = TRUE, verbose = FALSE)

Arguments

`sdf`	a `SigDF`
`mask`	include masked probes in Infinium-I probes. No big difference is noted in practice. More probes are generally better.
`verbose`	print more messages

Value

a SigDF after dye bias correction.

Examples

sesameDataCache() # if not done yet
sdf <- sesameDataGet('EPIC.1.SigDF')
sdf.db <- dyeBiasNL(sdf)
sdf <- sesameDataGet('EPIC.1.SigDF')
sdf <- dyeBiasCorrTypeINorm(sdf)

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.