gmqn_swan: GMQN + SWAN

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

Description

Using SWAN to conduct between array normalization and using BMIQ to conduct within array normalization. We slightly modified swan function in minfi package. When the signal value is less than 0, we make it equal to the non-zero minimum value not the background signal intensity.

Usage

gmqn_swan(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.