Cross-reactive probes/loci of methylation array

The maxprobes R package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K from papers. The cross-reactive probes/loci of EPIC/850K are from papers:

• Pidsley et al., Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology (2016)

• McCartney et al., Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip. Genomics Data (2016)

Those of 450K are from papers:

• Chen et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics (2013)

• Benton et al., An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biology (2015)

Install

if (! ("devtools" %in% installed.packages()) install.packages("devtools")
devtools::install_github("markgene/maxprobes")

Drop cross-reactive probes from minfi objects

Use the example data set in minfiData, which is 450K array comprising of 3 cancer samples and 3 normal controls.

suppressPackageStartupMessages(library(minfiData))
data(MsetEx)
MsetEx

#> class: MethylSet 
#> dim: 485512 6 
#> metadata(0):
#> assays(2): Meth Unmeth
#> rownames(485512): cg00050873 cg00212031 ... ch.22.47579720R
#>   ch.22.48274842R
#> rowData names(0):
#> colnames(6): 5723646052_R02C02 5723646052_R04C01 ...
#>   5723646053_R05C02 5723646053_R06C02
#> colData names(13): Sample_Name Sample_Well ... Basename filenames
#> Annotation
#>   array: IlluminaHumanMethylation450k
#>   annotation: ilmn12.hg19
#> Preprocessing
#>   Method: Raw (no normalization or bg correction)
#>   minfi version: 1.21.2
#>   Manifest version: 0.4.0

Call dropXreactiveLoci function to remove cross-reactive probes/loci:

library(maxprobes)
MsetEx_noXloci <- maxprobes::dropXreactiveLoci(MsetEx)
MsetEx_noXloci

#> class: MethylSet 
#> dim: 446571 6 
#> metadata(0):
#> assays(2): Meth Unmeth
#> rownames(446571): cg00212031 cg00213748 ... ch.22.47579720R
#>   ch.22.48274842R
#> rowData names(0):
#> colnames(6): 5723646052_R02C02 5723646052_R04C01 ...
#>   5723646053_R05C02 5723646053_R06C02
#> colData names(13): Sample_Name Sample_Well ... Basename filenames
#> Annotation
#>   array: IlluminaHumanMethylation450k
#>   annotation: ilmn12.hg19
#> Preprocessing
#>   Method: Raw (no normalization or bg correction)
#>   minfi version: 1.21.2
#>   Manifest version: 0.4.0

The probe/locus number (first number on dim row) drops from 485512 to 446571.

Obtain cross-reactive probe/loci IDs

If you need to get the list of probes/loci (e.g. you do not use minfi objects), you can get it by xreactive_probes function. It takes an argument array_type which is either "EPIC" or "450K", for EPIC/850K and 450K arrays, respectively.

xloci <- maxprobes::xreactive_probes(array_type = "EPIC")
length(xloci)

#> [1] 43256

xloci <- maxprobes::xreactive_probes(array_type = "450K")
length(xloci)

#> [1] 38941