QCfilter: Sample or CpG probe filter.

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Description

Filter low quality samples or CpGs, outlier samples or user specified samples or CpGs.

Usage

QCfilter(mdat,qcinfo=NULL,detPthre=0.000001,nbthre=3,samplethre=0.05,CpGthre=0.05,
         bisulthre=NULL,outlier=FALSE,outid=NULL, outCpG=NULL,plot=FALSE)

Arguments

mdat	An object of class MethylSet or beta value matrix.
qcinfo	An object outputed from function QCinfo
detPthre	Detection P value threshold to identify low quality data point
nbthre	Number of bead threshold to identify low quality data point
samplethre	Threshold to identify low quality samples, the percentage of low quality methylation data points across probes for each sample
CpGthre	Threshold to identify low quality probes, percentage of low quality methylation data points across samples for each probe
bisulthre	Threshold of bisulfite intensity for identification of low quality samples. By default, Mean - 3 x SD of sample bisufite control intensities will be used as the threshold.
outlier	If TRUE, outlier samples will be excluded.
outid	A list of user specified samples to be excluded.
outCpG	A list of user specified CpGs to be excluded.
plot	TRUE or FALSE, whether to produce quality checking plots.

Value

An same type object as input object after excluding low quality samples and CpGs

Figure "qc_sample.jpg": scatter plot for Percent of low quality data per sample and Average bisulfite conversion intensity

Figure "qc_CpG.jpg": histogram for Percent of low quality data per CpG.

Figure "freqpolygon_beta_beforeQC.jpg": distribution plot before filtering.

Figure "freqpolygon_beta_afterQC.jpg": distribution plot after filtering.

Author(s)

Zongli Xu

References

Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.

Examples

if(FALSE){
if (require(minfiData)) {
sheet <- read.metharray.sheet(file.path(find.package("minfiData"),"extdata"), pattern = "csv$")
rgSet <- read.metharray.exp(targets = sheet,extended = TRUE)
qcscore<-QCinfo(rgSet)
rgSet=QCfilter(rgSet,qcinfo=qcscore,outlier=TRUE)
}}

USCbiostats/ENmixUSC documentation built on June 1, 2019, 3:55 a.m.