In markgene/maxprobes: Methylation Array Cross-Reactive Probes

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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

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

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

The probe/locus number (first number on dim row) drops from r nrow(MsetEx) to r nrow(MsetEx_noXloci).

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)

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

markgene/maxprobes documentation built on May 17, 2019, 8:17 p.m.