gContainer-class {OSAT} | R Documentation |
"gContainer"
A class for storage information related to the experiment container setup.
setup.container(plate, n, batch = "plates", exclude = NULL)
plate |
A object of |
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. |
A gContainer
object.
Objects can be created by calls of the form
setup.container(plate, n, batch, exclude)
.
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.
signature(x = "gContainer")
: Return the
assembly of the plates used in the experiments.
signature(x = "gContainer")
: Return a data
frame that holds the layout of available wells in the container.
signature(object = "gContainer")
: Exclude some
wells/chips/plates from the container for randomization.
signature(x = "gContainer")
: Set the metadata.
signature(x = "gContainer")
: Get the metadata.
signature(object = "gContainer")
: A brief summary
of the container.
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)