QC: QC

In OSAT: OSAT: Optimal Sample Assignment Tool

Description

Provide a visual summary of the sample placement per plates, and Chi-squre test of dependence between plates and other considered variables from sample.

Usage

QC(object, main = NULL, ...)

Arguments

object	An object of class gExperimentSetup.
main	Mail title on the bar plot.
...	Additional plot parameters.

Examples

library("OSAT")
inPath <- system.file("extdata", package="OSAT")
pheno <- read.table(file.path(inPath, 'samples.txt'), header=TRUE, sep="\t")

## create object to hold sample information
gs <- setup.sample(pheno,  optimal=c("SampleType", "Race", "AgeGrp"), strata=c("SampleType") )
## create object that represents the used in the experiment
gc <- setup.container(IlluminaBeadChip96Plate, 6, batch='plates')
## create an optimized setup. 
# demonstration only. nSim=5000 or more are commonly used.
gSetup <- create.optimized.setup(sample=gs, container=gc, nSim=500)
QC(gSetup)

OSAT documentation built on Nov. 8, 2020, 5:48 p.m.