wateRmelon (version 1.16.0)

bscon: Calculate bisulphite conversion

Description

Uses control data from Infinium HumanMethylation450 BeadChip to calculate bisulfite conversion for each array

Usage

bscon(x, ...)  # S4 methods exist for RGChannelSet and MethyLumiset objects

Arguments

x

IDAT or report files containing 450k data

...

current methods have no optional arguments

Value

• A vector of percentage values referring to the bisulfite conversion levels of each array.

Details

This function uses the green and red channels reading of the type I and type II bisilfite conversion data to return the median bisulfite conversion percentage value for each array.

For the type I chemistry the beta values are calculated by dividing the first three probes of the green channel (C1, C2, C3) and the second three probes of the red channel (C4, C5, C6) by the sum of these probes and the unconverted probes of the green (U1, U2, U3) and the red (U4, U5, U6) channel.

The beta values from type II chemistry are calculated by dividing the methylated (red) channels by the sum of methylated (red) and unmethylated (green) channels.

Examples

library(wateRmelon)
data(melon)
bs <- bscon(melon)
bs