probeMasking: Cross-reactive and Polymorphic Probe Masking

In molepi/DNAmArray: Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach

Cross-reactive and Polymorphic Probe Masking

Description

This function masks cross-reactive and polymorphic probes as specified in Zhou et al. "Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes" (2017).

Usage

probeMasking(
  values,
  array = c("EPIC", "450K"),
  genome = c("hg19", "hg38"),
  verbose = TRUE
)

Arguments

values	beta or M values
array	EPIC or 450 array
genome	hg19 or hg38 as reference
verbose	default is TRUE

Details

Specification for both EPIC and HM450 arrays is possible and masking is genome dependent; different probes are filtered depending on whether hg38 or hg19 is specified as a reference.

Value

beta or M values

Author(s)

ljsinke

molepi/DNAmArray documentation built on Aug. 24, 2022, 1:42 p.m.