bactrl: bactrl

In metamaden/recountmethylation: Access and analyze public DNA methylation array data compilations

bactrl

Description

Get the BeadArray control metrics from HM450K platform red/grn signals.

Usage

bactrl(
  cdf = NULL,
  baset = "reduced",
  rg = NULL,
  rs = NULL,
  gs = NULL,
  baseline = 3000,
  biotin.baseline = 1
)

Arguments

cdf	Control probe annotations (optional, NULL, data.frame, cols = properties, rows = probes).
baset	Either the most informative BeadArray metrics (a.k.a. "reduced" set, 5 metrics, recommended), or the full set of 17 metrics ("all").
rg	An RGChannelSet object (optional, NULL).
rs	Red signal data (optional, NULL, data.frame, columns are probes, rows are samples, column names are addresses, rownames are samples/GSM IDs).
gs	Green signal data (optional, NULL, data.frame, columns are probes, rows are samples, column names are addresses, rownames are samples/GSM IDs).
baseline	Baseline measure for signals (integer, 3000).
biotin.baseline	Baseline to use for biotin controls (integer, 1).

Details

This function calculates the BeadArray quality metrics based on Illumina's documentation and previous work (see references). Based on previous work, this function can calculate the full set of 17 metrics (e.g. baset = 'all'), or the reduced set of 5 metrics (e.g. baset = 'reduced'), where the latter is recommended for most purposes. For additional details, consult the BeadArray metrics vignette in this package.

Value

Matrix of BeadArray signal values

References

1. S. K. Maden, et. al., "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus," NAR Genomics and Bioinformatics, Volume 3, Issue 2, June 2021

2. Illumina, “Illumina Genome Studio Methylation Module v1.8,” Nov. 2010.

3. Illumina, “BeadArray Controls Reporter Software Guide,” Oct. 2015.

4. J. A. Heiss and A. C. Just, “Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO,” Clinical Epigenetics, vol. 10, June 2018. '

See Also

bathresh

Examples

dir <- system.file("extdata", "bactrl", package = "recountmethylation")
rgf <- get(load(file.path(dir, "rgf-cgctrl-test_hm450k-minfidata.rda")))
mba <- bactrl(rg = rgf)

metamaden/recountmethylation documentation built on Jan. 5, 2023, 9:56 a.m.