qPCRset-class {HTqPCR} | R Documentation

## 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))

[Package HTqPCR version 1.41.0 Index]