gContainer-class: Class '"gContainer"'

In llrs/OSAT: OSAT: Optimal Sample Assignment Tool

Description

A class for storage information related to the experiment container setup.

Usage

setup.container(plate, n, batch = "plates", exclude = NULL)

Arguments

plate	A object of gPlate class or its expanded class.
n	Number of plates used in the experiment.
batch	The level where batch effect is considered.
exclude	A data frame indicate location of wells in the container that should be excluded from sample assigment in the experiment.

Value

A gContainer object.

Objects from the Class

Objects can be created by calls of the form setup.container(plate, n, batch, exclude).

Slots

plate:

Object of class "gPlate". Plate used in the experiment.

n:

Object of class "integer". Number of plate used.

batch:

Object of class "character". On what level batch effect are considered. Could be "plates" or "chips".

exclude:

Object of class "data.frame". A data frame indicate wells that should be excluded from the sample Assignment.

data:

Object of class "list". A list holds summaries and other useful informaiton.

metadata:

Object of class "list". A list for a brief description and other useful informtion.

Methods

get.gAssembly

signature(x = "gContainer"): Return the assembly of the plates used in the experiments.

getLayout

signature(x = "gContainer"): Return a data frame that holds the layout of available wells in the container.

exclude<-

signature(object = "gContainer"): Exclude some wells/chips/plates from the container for randomization.

metadata<-

signature(x = "gContainer"): Set the metadata.

metadata

signature(x = "gContainer"): Get the metadata.

show

signature(object = "gContainer"): A brief summary of the container.

Examples

library("OSAT")
# a container consist of 6 predefined Illumina plates with 96 wells each
gc <- setup.container(IlluminaBeadChip96Plate, 6, batch='plates')
gc

# to exclude first wells on first chips of each plate.
(excludedWells <- data.frame(plates=1:6, chips=rep(1,6), wells=rep(1,6)) )
gc3 <- setup.container(IlluminaBeadChip96Plate, 6, batch='plates', exclude=excludedWells)

llrs/OSAT documentation built on May 23, 2019, 7:18 a.m.