rmSNPandCH: Filter probes

In rcavalcante/DMRcate: Methylation array and sequencing spatial analysis methods

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.

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 Pidsley and Zotenko et al. (2016) for EPIC or Chen et al. (2013) for 450K to be cross-reactive with areas of the genome not at the site of interest. Many of these sites are on the X-chromosome, leading to potential confounding if the sample group is a mix of males and females. There are 63,707 probes in total in this list. 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 (7 in total of the 153,113), 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 J. 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). http://supportres.illumina.com/documents/myillumina/88bab663-307c-444a-848e-0ed6c338ee4d/humanmethylation450_15017482_v.1.2.snpupdate.table.v3.txt

Examples

## Not run: 
data(dmrcatedata)
myMs <- logit2(myBetas)
myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)

## End(Not run)

rcavalcante/DMRcate documentation built on May 21, 2019, 10:13 a.m.