control_probe_intensities: Get control probes and their raw intensities.

In markgene/yamat: Yet Another Methylation Array Toolkit

Get control probes and their raw intensities.

Description

Notes:

Usage

control_probe_intensities(x)

Arguments

x	An object of RGChannelSet-class.

Details

1. There are conflictings between Illumina Infinium HD Methylation Assay (Document # 15019519 v10) and DRAGEN documentation. The Illumina Infinium HD Methylation Assay said C1-C3 and U1-U3 are for bisulfite conversion I green channel. But based on DRAGEN document, C3 and U3 are actually on red channel. I use probes C1-C2 and U1-U2 in this function.

2. There are conflictings between Illumina Infinium HD Methylation Assay (Document # 15019519 v10) and [DRAGEN documentation](https://help.dragenarray.illumina.com/product-guides/output-files#methyl_qc_report). The Illumina Infinium HD Methylation Assay said C4-C6 and U4-U6 are for bisulfite conversion I green channel. But based on DRAGEN document, C3 and U3 are actually on red channel too. I use probes C3-C6 and U3-U6 in this function.

3. There are five extra NP (G) probes of uncertain use, which I do not use for non-polymorphic probe QC metric computation.

Value

A data.frame containing the following columns: Address, Type, Color, ExtendedType, Channel, Expected_Grn, Expected_Red, Sample, Group, Intensity.

markgene/yamat documentation built on Aug. 26, 2024, 11:56 p.m.