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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:

Those of 450K are from papers:

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

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maxprobes's Issues

Error while installing

Hello,
First, thanks for this excellent idea for a package.
I've tried to install the package by downloading the Zip file then using the devtools function install local ( I don't have access to install::remote) and I've encountered this Error :

* installing *source* package 'cnv.methyl' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Error in read.table(...) : more columns than column names
ERROR: lazydata failed for package 'cnv.methyl'

Is there something I did wrong ?
Kind regards

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