rmSNPandCH: Filter probes

In timpeters82/DMRcate-devel: Methylation array and sequencing spatial analysis methods

Filter probes

Description

Filters a matrix of M-values (or beta values) by distance to SNP/variant. Also (optionally) removes cross-hybridising probes and sex-chromosome probes. Also removes “rs” and “nv” probes from the matrix.

Usage

rmSNPandCH(object, dist = 2, mafcut = 0.05, and = TRUE, rmcrosshyb = TRUE, 
           rmXY = FALSE) 

Arguments

object	A matrix of M-values or beta values, with unique Illumina probe IDs as rownames.
dist	Maximum distance (from CpG to SNP/variant) of probes to be filtered out. See details for when Illumina occasionally lists a CpG-to-SNP distance as being < 0.
mafcut	Minimum minor allele frequency of probes to be filtered out.
and	If TRUE, the probe must have at least 1 SNP binding to it that satisfies both requirements in dist and mafcut for it to be filtered out. If FALSE, it will be filtered out if either requirement is satisfied. Default is TRUE.
rmcrosshyb	If TRUE, filters out probes found by Peters et al. (2024) (EPICv2), Pidsley and Zotenko et al. (2016) (EPICv1) or Chen et al. (2013) (450K) to be cross-reactive with areas of the genome not at the site of interest. Default is TRUE.
rmXY	If TRUE, filters out probe hybridising to sex chromosomes. Or-operator applies when combined with other 2 filters.

Details

Probes in -1:dist will be filtered out for any integer specification of dist. When a probe is listed as being “-1” nucleotides from a SNP, that SNP is immediately adjacent to the end of the probe, and is likely to confound the measurement, in addition to those listed as 0, 1 or 2 nucleotides away. See vignette for further details.

Value

A matrix, attenuated from object, with rows corresponding to probes matching user input filtered out.

Author(s)

Tim Peters <[e-mail]>

References

Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, Van Dijk S, Muhlhausler B, Stirzaker C, Clark SJ. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology. 2016 17(1), 208.

Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013 Jan 11;8(2).

Peters, T.J., Meyer, B., Ryan, L., Achinger-Kawecka, J., Song, J., Campbell, E.M., Qu, W., Nair, S., Loi-Luu, P., Stricker, P., Lim, E., Stirzaker, C., Clark, S.J. and Pidsley, R. (2024). Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 25, 251. doi:10.1186/s12864-024-10027-5.

Examples

library(ExperimentHub)
eh <- ExperimentHub()
ALLbetas <- eh[["EH9451"]]
ALLbetas <- ALLbetas[1:1000,]
ALLMs <- minfi::logit2(ALLbetas)
ALLMs.noSNPs <- rmSNPandCH(ALLMs, rmcrosshyb = FALSE)

timpeters82/DMRcate-devel documentation built on Dec. 19, 2024, 11:14 a.m.