cellData-class: The cellData class

Description Usage Arguments Value Slots Methods Examples

Description

The main class used in OperaMate to hold all levels of experiment data of a specific type.

Usage

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cellData(name, positive.ctr = character(0), negative.ctr = character(0),
  expwell = character(0),
  norm.method = getOption("opm.normalization.method"),
  QC.threshold = getOption("opm.QC.threshold"))

## S4 method for signature 'cellData,character,ANY'
x[i]

## S4 method for signature 'cellData'
show(object)

Arguments

name

character, the analyzed item

positive.ctr

a character vector, the positive control well IDs, e.g. c("E05", "E06")

negative.ctr

a character vector, the positive control well IDs, e.g. c("B05", "B06")

expwell

include all wells except control and neglect.well if NULL

norm.method

character the normalization method.

QC.threshold

numeric, the thresholds in the quality control.

x

a cellData object

i

a requested slot name

object

a cellData class

Value

a cellData object

Slots

name

character, one parameter in the Columbus system report.

posctrwell

a character vector, the positive control well IDs, e.g. B05.

negctrwell

a character vector, the negative control well IDs, e.g. B05.

expwell

a character vector, the sample well IDs, e.g. C15.

cellNum

matrix, cell numbers

origin.data

a numeric matrix, the raw data matrix with rows the well IDs and columns the plate IDs.

norm.data

a numeric matrix, the normalized data.

qc.data

a numeric matrix, the data after quality control, with the rows are "barcode:wellID" and columns are the data of all replicated samples and their means, and if they have passed the quality control.

norm.method

character the normalization method.

QC.threshold

numeric, the thresholds in the quality control.

plate.quality

a logical matrix, the quality data with the rows are the barcode and columns are the replicateIDs.

plate.quality.data

a list of plate correlations and plate z' factors

Sig

a list of the following components:

  • SigMat:a logic matrix marking the high and low expressed hits

  • threshold:the threshold of the high and low expressed hits

  • stats:the numbers of the high and low expressed hits

  • pvalue:the pvalue of each sample by t tests

Methods

Constructor

cellData(name, positive.ctr = character(0), negative.ctr = character(0), expwell = character(0), norm.method = getOption("opm.normalization.method"), QC.threshold = getOption("opm.QC.threshold").

Show

signature(object="cellLoad"). Displays object content as text.

Accessor

x[i]. x: a cellData object; i: character, a cellData slot name.

Examples

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oneCell <- cellData(name = "Average Intensity of Nuclei",
positive.ctr = c("H02", "J02", "L02"),
negative.ctr = c("C23", "E23", "G23"))
oneCell
oneCell["name"]

Bioconductor-mirror/OperaMate documentation built on May 31, 2017, 9:38 p.m.