plotCtrl

An object of class <code>RGChannelSet</code>.

rgSet

A list of sample ids in the order user specified. The list can be a subset of the samples in input dataset. If an id list is provided, all plots will be produced in the order of the list. The default is NULL.

IDorder


Intensity data are ploted for all internal control probe types on the Illumina Infinium HumanMethylation450 or MethylationEPIC BeadChip. These figures can be used to check data quality and experimental procedures. 


Illumina Methylation BeadChip array measurements have
intrinsic levels of background noise that degrade methylation measurement.
The ENmix package provides an efficient data pre-processing tool designed
to reduce background noise and improve signal for DNA methylation estimation.
Several efficient novel methods were incorporated in the package: ENmix is a
model based background correction method that can significantly improve
accuracy and reproducibility of methylation  measures; RCP taking
advantage of the high spatial correlation of DNA methylation levels between
nearby type I and II probe pairs to reduce probe type bias and improve
data quality on type II probe measures.The data structure used by the
ENmix package is compatible with
several other related R packages, such as minfi, wateRmelon and ChAMP,
providing straightforward integration of ENmix-corrected datasets for
subsequent data analysis. The software is designed to support large
scale data analysis, and provides multi-processor parallel computing
wrappers for some commonly used but computation intensive data
preprocessing methods.
In addition ENmix package has selectable complementary functions for
efficient data visualization (such as data distribution plotting),
quality control (identification and filtering of low quality data points,
samples, probes, and outliers, along with imputation of missing values),
inter-array normalization (3 different quantile normalizations),
identification of probes with multimodal distributions due to SNPs and
other factors, and exploration of data variance structure using principal
component regression analysis plots. Together these provide a set of
flexible and transparent tools for preprocessing of EWAS data in a
computationally-efficient and user-friendly package.

Zongli Xu

ENmix

Data preprocessing and quality control for Illumina
HumanMethylation450 and MethylationEPIC BeadChip

plotCtrl function

Intensity data are ploted for all internal control probe types on the Illumina Infinium HumanMethylation450 or MethylationEPIC BeadChip. These figures can be used to check data quality and experimental procedures.

plotCtrl: Plot internal controls of 450K or MethylationEPIC BeadChip.

Description

Usage

Arguments

Value

References

Examples