qPCRset-class {HTqPCR} | R Documentation |
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 can be created by calls of the form new("qPCRset", assayData, phenoData, featureData, experimentData, annotation, protocolData, ...)
or using readCtData
.
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.
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
signature(x = "qPCRset")
: Subsets by genes or samples.
signature(object = "qPCRset")
: Extracts the Ct matrix. Is identical to getCt
signature(object = "qPCRset", value = "matrix")
: Replaces the Ct matrix. Is identical to setCt<-
signature(object = "qPCRset")
: Extracts the Ct matrix. Is identical to exprs
.
signature(object = "qPCRset", value = "matrix")
: Replaces the Ct matrix. Is identical to exprs<-
.
signature(object = "qPCRset")
: Extracts the features (gene names) on the card.
signature(object = "qPCRset", value = "character")
: Replaces the features (gene names) on the card.
signature(object = "qPCRset")
: Extracts the sample names.
signature(object = "qPCRset", value = "character")
: Replaces the sample names.
signature(object = "qPCRset")
: Extracts the different types of features on the card, such as controls and target genes.
signature(object = "qPCRset", value = "factor")
: Replaces the feature type for each gene.
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.
signature(object = "qPCRset", value = "character")
: Replaces the position of each feature (gene) on the card.
signature(object = "qPCRset")
: Extracts the feature class for each gene.
signature(object = "qPCRset", value = "factor")
: Replaces the feature class for each gene, for example if it is a marker, transcription factor or similar.
signature(object = "qPCRset")
: Extracts the category of each Ct value.
signature(object = "qPCRset", value = "data.frame")
: Replaces the category of each Ct value.
signature(object = "qPCRset")
: Extracts the flag of each Ct value.
signature(object = "qPCRset")
: Replaces the flag of each Ct value.
signature(object = "qPCRset")
: Extracts information about the number of wells on the card.
signature(object = "qPCRset")
: Extracts information about the number of samples in the set.
signature(object = "qPCRset")
: Extracts data frame containing information about the history of the object (which operations have been performed on it).
signature(object = "qPCRset")
: Add information about the history of the object.
signature(object = "qPCRset")
: Displays some abbreviated information about the data object.
signature(object = "qPCRset")
: Displays a summary of the Ct values from each sample.
Heidi Dvinge
# 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))