get_bactrl: Get control probe metrics from matrices of red/grn signal

In metamaden/rmpipeline: Process DNAm array IDATs into database files

Get control probe metrics from matrices of red/grn signal

Description

This resource takes guidance from 3 key sources: the Illumina GenomeStudio Methylation Module (v1.8, source 1), the BeadArray Controls Reporter Software Guide (v00, source 2), and the ewastools resource (v1.5, source 3). Notes on how function relates to these sources follows:

* Use C and U 1-3 and 4-6 for Bisulfite Conversion I per source 2, source 3 only uses 1-2/4-5, and may have string matching error

* Use probe address "34648333" and "43603326" (DNP, Biotin subtype) for Biotin 'Staining Background where appropriate, per sources 2 and 3;

* To offset many Inf/-Inf values due to 0 background signal, set a special Biotin specific baseline offset (default: 1) in denom of Biotin red/grn Bkg value. No offset specified in source 2;

* For Specificity I, use PM, MM 1-3 for grn, 4-6 for red (per source 3, source 2 ambiguous);

* For Specificity II, use just probes S1-3, as probe S4 unavailable in control probe annotation (per source 2, corroborated in source 3)

* Note definition for background is ambiguous (can be either Red or Grn channel, from extension), per source 2; source 3 uses extension Grn A/T probes for system background

* Note additional source 2 metrics using background (e.g. specificity background/U1-3) currently not calculated by 'bactrl()'.

Usage

get_bactrl(
  rgset,
  baseline = 3000,
  biotin.baseline = 1,
  verbose = TRUE,
  cnv = c("restoration.grn", "biotin.stain.red", "biotin.stain.grn",
    "specificityI.red", "specificityI.grn", "specificityII", "extension.red",
    "extension.grn", "hyb.hi.med", "hyb.med.low", "target.removal.1", "target.removal.2",
    "bisulfite.conv.I.red", "bisulfite.conv.I.grn", "bisulfite.conv.II",
    "nonpolymorphic.red", "nonpolymorphic.grn")
)

Arguments

rgset	RGChannelSet objet containing control probe signals.
baseline	Baseline measure for signals (integer, 3000).
biotin.baseline	Baseline to use for biotin controls (integer, 1).
verbose	Whether to show status messages (TRUE, boolean).
cnv	Vector of control assay names for columns in returned table.

Value

Table of BeadArray control assay signals.

See Also

bathresh

metamaden/rmpipeline documentation built on Jan. 12, 2023, 3:20 p.m.