chipAddressToSignal: Lookup address in one sample

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Lookup address and transform address to probe

Usage

chipAddressToSignal(dm, manifest, controls = NULL)

Arguments

dm	data frame in chip address, 2 columns: cy3/Grn and cy5/Red
manifest	a data frame with columns Probe_ID, M, U and col
controls	a data frame with columns Address and Name. This is optional but might be necessary for some preprocessing methods that depends on these control probes. This is left for backward compatibility. Updated version should have controls consolidated into manifest.

Details

Translate data in chip address to probe address. Type I probes can be separated into Red and Grn channels. The methylated allele and unmethylated allele are at different addresses. For type II probes methylation allele and unmethylated allele are at the same address. Grn channel is for methylated allele and Red channel is for unmethylated allele. The out-of-band signals are type I probes measured using the other channel.

Value

a SigSet, indexed by probe ID address

sesame documentation built on Nov. 15, 2020, 2:08 a.m.