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