MSAroboticPlate-class: Class '"MSAroboticPlate"'

In OSAT: OSAT: Optimal Sample Assignment Tool

Description

A class store layout information of MSA robotic loader plate.

Extends

Class "gArray", directly.

Methods

map.to.MSA

signature(x = "data.frame", y = "MSAroboticPlate"): Return a data frame that assign samples (represented by the input data frame) to MSA robotic plate sequentially.

map.to.MSA

signature(x = "gExperimentSetup", y = "MSAroboticPlate"): Return a data frame that assign samples from an gExperimentSetup object to MSA robotic plate.

show

signature(object = "MSAroboticPlate"): Shows the layout of the plate.

Predefined objects

MSA4.plate: A predeined object of class MSAroboticPlate that represent a 96 position plate.

BeadChip96ToMSA4MAPMap: The loading order a MSA4 robotic loader used to load BeadChips.

See Also

gExperimentSetup

Examples

library("OSAT")
# data as an example
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") )
gs

gc <- setup.container(IlluminaBeadChip96Plate, 6, batch='plates')
gc

gSetup <- create.optimized.setup(sample=gs, container=gc, nSim=100)
out <- map.to.MSA(gSetup, MSA4.plate)

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