RTqPCRBatch-class: Class RTqPCRBatch

In NPhogat/RTqPCR: A work flow for analysis and normalization of pre-processing RT-qPCR data

Description

Class to Contain and Describe raw and normalised qPCR Data, as Cq or delta-Cq values. Extends eSet

Creating Objects

new("RTqPCRBatch")

Slots

assayData:

Object of class AssayData containing the raw data, which will be at minimum a matrix of Cq values. This slot can also hold a matrix of well.info values if these are present in the input file.

phenoData:

Object of class AnnotatedDataFrame containing phenotypic data for the samples.

annotation

A character string identifying the annotation that may be used for the RTqPCRBatch instance.

protocolData:

Object of class AnnotatedDataFrame containing protocol data for the samples.

featureData

Object of class AnnotatedDataFrame containing feature-level (e.g., probeset-level) information.

experimentData:

Object of class "MIAME" containing experiment-level information.

.__classVersion__:

Object of class Versions describing the R and Biobase version number used to create the instance. Intended for developer use.

Methods

exprs

signature(object = "RTqPCRBatch"): extracts the Cq expression matrix.

exprs<-

signature(object = "RTqPCRBatch", value = "matrix"): replaces the Cq expression matrix.

se.exprs

signature(object = "RTqPCRBatch"): extracts the expression matrix with SDs of Cq values.

se.exprs<-

signature(object = "RTqPCRBatch", value = "matrix"): replaces the expression matrix with SDs of Cq values.

exprs.well.order

signature(object = "RTqPCRBatch"): extracts the Cq well order matrix (if it exists).

exprs.well.order<-

signature(object = "RTqPCRBatch", value = "matrix"): replaces the Cq well order matrix.

effs

signature(object = "RTqPCRBatch"): extracts the efficiency matrix (if it exists).

effs<-

signature(object = "RTqPCRBatch", value = "matrix"): replaces the efficiency matrix.

se.effs

signature(object = "RTqPCRBatch"): extracts the matrix with the standard errors/deviations of the efficiencies (if it exists).

se.effs<-

signature(object = "RTqPCRBatch", value = "matrix"): replaces the matrix with the standard errors/deviations of the efficiencies.

Note

This class is described in detail in the vignette.

Author(s)

Navneet Phogat, Matthias Kohl, [e-mail]

References

Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.

See Also

eSet

NPhogat/RTqPCR documentation built on July 12, 2020, 12:56 p.m.