Class "qPCRset"

Description

This is a class for containing the raw or normalized cycle threshold (Ct) values and some related quality information. It is suitable for TaqMan Low Density Arrays or any other type of (high-throughput) qPCR data, where gene expression is measured for any number of genes, across several samples/conditions. It inherits from eSet for microarray data.

Objects from the Class

Objects can be created by calls of the form new("qPCRset", assayData, phenoData, featureData, experimentData, annotation, protocolData, ...) or using readCtData.

Slots

CtHistory:

Object of class "data.frame" indicating how the data has been read in, normalized, filtered etc. Gives the exact commands used during these operations.

assayData:

Object of class "AssayData", containing the Ct values.

phenoData:

Object of class "AnnotatedDataFrame", where information about samples can be added.

featureData:

Object of class "AnnotatedDataFrame", where information about features can be added. If the object is from readCtData, the featureData will contain the columns 'featureName', 'featurePos' and 'featureType'.

experimentData:

Object of class "MIAxE", where details about the experiment can be stored.

annotation:

Object of class "character", where the name of the qPCR assay can be stored.

protocolData:

Object of class "AnnotatedDataFrame", where details of the protocol can be stored.

.__classVersion__:

Object of class "Versions".

Furthermore, the following information is contained within the object.

flag:

Object of class "data.frame" containing the flag for each Ct value, as supplied by the input files.

featureCategory:

Object of class "data.frame" representing the quality of the measurement for each Ct value, such as "OK", "Undetermined" or "Unreliable" if the Ct value is considered too high.

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

[

signature(x = "qPCRset"): Subsets by genes or samples.

exprs

signature(object = "qPCRset"): Extracts the Ct matrix. Is identical to getCt

exprs<-

signature(object = "qPCRset", value = "matrix"): Replaces the Ct matrix. Is identical to setCt<-

getCt

signature(object = "qPCRset"): Extracts the Ct matrix. Is identical to exprs.

setCt<-

signature(object = "qPCRset", value = "matrix"): Replaces the Ct matrix. Is identical to exprs<-.

featureNames

signature(object = "qPCRset"): Extracts the features (gene names) on the card.

featureNames<-

signature(object = "qPCRset", value = "character"): Replaces the features (gene names) on the card.

sampleNames

signature(object = "qPCRset"): Extracts the sample names.

sampleNames<-

signature(object = "qPCRset", value = "character"): Replaces the sample names.

featureType

signature(object = "qPCRset"): Extracts the different types of features on the card, such as controls and target genes.

featureType<-

signature(object = "qPCRset", value = "factor"): Replaces the feature type for each gene.

featurePos

signature(object = "qPCRset"): Extracts the position of each feature (gene) on the assay, representing the location "well" (such as well A1, A2, ...). If data does not come from a card format, the positions will be given consecutive names.

featurePos<-

signature(object = "qPCRset", value = "character"): Replaces the position of each feature (gene) on the card.

featureClass

signature(object = "qPCRset"): Extracts the feature class for each gene.

featureClass<-

signature(object = "qPCRset", value = "factor"): Replaces the feature class for each gene, for example if it is a marker, transcription factor or similar.

featureCategory

signature(object = "qPCRset"): Extracts the category of each Ct value.

featureCategory<-

signature(object = "qPCRset", value = "data.frame"): Replaces the category of each Ct value.

flag

signature(object = "qPCRset"): Extracts the flag of each Ct value.

flag<-

signature(object = "qPCRset"): Replaces the flag of each Ct value.

n.wells

signature(object = "qPCRset"): Extracts information about the number of wells on the card.

n.samples

signature(object = "qPCRset"): Extracts information about the number of samples in the set.

getCtHistory

signature(object = "qPCRset"): Extracts data frame containing information about the history of the object (which operations have been performed on it).

setCtHistory<-

signature(object = "qPCRset"): Add information about the history of the object.

show

signature(object = "qPCRset"): Displays some abbreviated information about the data object.

summary

signature(object = "qPCRset"): Displays a summary of the Ct values from each sample.

Author(s)

Heidi Dvinge

Examples

# The data format
data(qPCRraw)
show(qPCRraw)
getCtHistory(qPCRraw)
showClass("qPCRset")
str(qPCRraw)
# Information about samples
phenoData(qPCRraw)
pData(qPCRraw)
pData(qPCRraw)[,"Rep"] <- c(1,1,2,2,3,3)
# Information about features
featureData(qPCRraw)
head(fData(qPCRraw))