get_crossreactive_cpgs: get_crossreactive_cpgs

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

get_crossreactive_cpgs

Description

Get cross-reactive CpG probe IDs for Illumina BeadArray platforms.

Usage

get_crossreactive_cpgs(probeset = "all")

Arguments

probeset

Specify the set of probes to filter ("all", "hm450k", "epic", "chen", "pidlsey", "illumina").

Details

Prior work showed significant cross-reactivity at subsets of CpG probes on Illumina's BeadArray platforms, including HM450K and EPIC. This was primarily due to the probe sequence, as the targeted 50-bp sequence can be either too short or too degenerate to bind a particular DNA region with high specificity. This can cause cross-reaction with off-target DNA locations, including at entirely different chromosomes than the target sequence. Consult the individual publication sources for details about the identification and consequences of cross-reactive CpG probes.

You can retrieve a cross-reactive probe set in a variety of ways. For instance, declare the publication source with either "chen" (for Chen et al 2013), "pidsley" (for Pidsley et al 2016), or "illumina" (for official Illumina documentation), or declare the platform category as either "all" (both HM450K and EPIC), "hm450k", or "epic."

Value

Vector of cross-reactive CpG probe IDs.

References

1. Yi-an Chen, Mathieu Lemire, Sanaa Choufani, Darci T. Butcher, Daria Grafodatskaya, Brent W. Zanke, Steven Gallinger, Thomas J. Hudson & Rosanna Weksberg (2013) Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray, Epigenetics, 8:2, 203-209, DOI: 10.4161/epi.23470

2. Pidsley, R., Zotenko, E., Peters, T.J. et al. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol 17, 208 (2016). https://doi.org/10.1186/s13059-016-1066-1

See Also

bactrl, get_qcsignal

Examples

length(get_crossreactive_cpgs("all"))      # 46324
length(get_crossreactive_cpgs("hm450k"))   # 30540
length(get_crossreactive_cpgs("epic"))     # 43410
length(get_crossreactive_cpgs("chen"))     # 29233
length(get_crossreactive_cpgs("pidsley"))  # 43254
length(get_crossreactive_cpgs("illumina")) # 1031

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