UniD.dataqc: Probe quality evaluation

In JieYang031/UniD: Unified Diagnostic Platform for Gliomas

Description

Used to evaluate the probe quality in term of probe detection p-value and beadcount. For probes which failed the cut point, they will be set as missing value. The data with missing value will be returned/saved as beta value.

Usage

UniD.dataqc(loading = loading, outDir, detP.cut = 0.05, bc.cut = 3,
  arrayType, write)

Arguments

loading	List generated from the UniD.load()
outDir	directory where output data should be saved if write = T
detP.cut	The cut point for detection P-value, default is 0.05. If the probe's detection p-value > 0.05, the probe will be set as missing value in a sample-wise fashion.
bc.cut	The cut point for beadcount per probe, default is 3. If beadcount < 3, the probe will be set as missing value sample-wise. control probes
arrayType	the platform which raw data generated, can be "450k" or "EPIC"
write	whether the output should be saved, highly recommended

Value

A data frame with beta values for all samples and probes.

Examples

## Not run: 
Beta.raw <- UniD.dataqc(loading = loading, outDir = "~/Desktop/output/",
detP.cut = 0.05, bc.cut = 3, arrayType = "450k", write = T)

Beta.raw <- UniD.dataqc(loading = loading,  outDir = NULL, detP.cut = 0.05,
bc.cut = 3, arrayType = "450k", write = F)

## End(Not run)

JieYang031/UniD documentation built on May 5, 2021, 5:16 p.m.