gmqn_bmiq: GMQN + BMIQ

In MengweiLi-project/gmqn: Gaussian Mixture Quantile Normalization (GMQN)

Description

Using GMQN to conduct between array normalization and using BMIQ to conduct within array normalization. The BMIQ was developed by Andrew Teschendorff in 2013 and this implementation is the based on the version modified by Steve Horvath. I also removed and modified some parameters to simplify the function.

Usage

gmqn_bmiq(m, um, probe, type = "450k", ref = "default",
  verbose = TRUE)

Arguments

m	The vector of methylation signal intensities.
um	The vector of umethylation signal intensities.
probe	the probe id for m and um.
type	The type of methylation array which can be '450k'(default) or '850k'
ref	The reference used to normalize data. By default, it uses the reference set up from GSE105018 which is also used in EWAS Datahub.

Value

A data frame contains normalized m and um, p value, and DNA methylation level

MengweiLi-project/gmqn documentation built on Feb. 26, 2020, 11:35 a.m.