QCinfo: QC information.

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

Description

Extract informations for data quanlity controls: detection P values, number of beads and averaged bisulfite conversion intensity. The function can also identify low quality samples and probes, as well as outlier samples based on total intensity or beta value distribution.

Usage

QCinfo(rgSet, detPthre=0.000001, nbthre=3, samplethre=0.05, CpGthre=0.05,
       bisulthre=NULL, outlier=TRUE, distplot=TRUE)

Arguments

rgSet	An object of class RGChannelSetExtended.
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 in total intensity or beta value distribution will be idenfied and classified as bad samples.
distplot	TRUE or FALSE, whether to produce beta value distribution plots before and after QC.

Value

detP: a matrix of detection P values

nbead: a matrix for number of beads

bisul: a vector of averaged intensities for bisulfite conversion controls

badsample: a list of low quality or outlier samples

badCpG: a list of low quality CpGs

outlier_sample: a list of outlier samples

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)
}}

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