gContainer-class: Class '"gContainer"'

In 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)

Example output

An object of class "gContainer"

It consists of 6 IlluminaBeadChip96Plate plates.
The block level is set at plates level.
  plates cFactor Freq
1      1       1   96
2      2       2   96
3      3       3   96
4      4       4   96
5      5       5   96
6      6       6   96
The container layout is
@data$container
  plates chipRows chipColumns chips rows columns wells chipID rowID wellID
1      1        1           1     1    1       1     1      1     1      1
2      1        1           1     1    2       1     2      1     1      2
3      1        1           1     1    3       1     3      1     1      3
4      1        1           1     1    4       1     4      1     1      4
5      1        1           1     1    5       1     5      1     1      5
6      1        1           1     1    6       1     6      1     1      6
  cFactor
1       1
2       1
3       1
4       1
5       1
6       1

 ... 
    plates chipRows chipColumns chips rows columns wells chipID rowID wellID
571      6        2           4     8    1       2     7     48   286    571
572      6        2           4     8    2       2     8     48   286    572
573      6        2           4     8    3       2     9     48   286    573
574      6        2           4     8    4       2    10     48   286    574
575      6        2           4     8    5       2    11     48   286    575
576      6        2           4     8    6       2    12     48   286    576
    cFactor
571       6
572       6
573       6
574       6
575       6
576       6
  plates chips wells
1      1     1     1
2      2     1     1
3      3     1     1
4      4     1     1
5      5     1     1
6      6     1     1

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