QCfilter {ENmix} | R Documentation

## Sample or CpG probe filter.

### 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)
    }}

[Package ENmix version 1.21.6 Index]