# Automated analysis of qPCR data

## Documentation for package ‘HTqPCR’ version 1.0.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

HTqPCR-package | Analysis of High-Throughput qPCR data (HTqPCR)
clusterCt | Clustering of qPCR Ct values
exprs,qPCRset-method | Class "qPCRset"
exprs<-,qPCRset,matrix-method | Class "qPCRset"
featureCategory | Class "qPCRset"
featureCategory<- | Class "qPCRset"
featureClass | Class "qPCRset"
featureClass<- | Class "qPCRset"
featureNames,qPCRset-method | Class "qPCRset"
featureNames<-,qPCRset,character-method | Class "qPCRset"
featurePos | Class "qPCRset"
featurePos<- | Class "qPCRset"
featureType | Class "qPCRset"
featureType<- | Class "qPCRset"
filterCategory | Filter Ct values based on their feature categories.
filterCtData | Filter out features (genes) from qPCR data.
flag | Class "qPCRset"
flag<- | Class "qPCRset"
heatmapSig | Heatmap of deltadeltaCt values from qPCR data.
HTqPCR | Analysis of High-Throughput qPCR data (HTqPCR)
limmaCtData | Differentially expressed features with qPCR: limma
n.samples | Class "qPCRset"
n.wells | Class "qPCRset"
normalizeCtData | Normalization of Ct values from qPCR data.
normalized | Class "qPCRset"
plotCtBoxes | Boxplots for qPCR Ct values.
plotCtCard | Image plot of qPCR Ct values from a card format
plotCtCategory | Summarising the feature categories for Ct values.
plotCtCor | Correlation between Ct values from qPCR data
plotCtDensity | Distribution plot for qPCR Ct values.
plotCtHeatmap | Heatmap of qPCR Ct values.
plotCtHistogram | Histrogram of Ct values from qPCR experiments.
plotCtLines | Plotting Ct values from qPCR across multiple samples.
plotCtOverview | Overview plot of qPCR Ct values across multiple conditions.
plotCtPairs | Pairwise scatterplot of multiple sets of Ct values from qPCR data.
plotCtPCA | PCA for qPCR Ct values.
plotCtReps | Scatter plot of features analysed twice during each qPCR experiment.
plotCtRQ | Plot the relative quantification of Ct values from qPCR experiments.
plotCtScatter | Scatterplot of two sets of Ct values from qPCR data.
plotCtSignificance | Barplot with Ct values between genes from qPCR.
plotCVBoxes | Boxplots of CV for qPCR Ct values.
qPCRpros | Example processed qPCR data
qPCRraw | Example raw qPCR data.
qPCRset-class | Class "qPCRset"
readCtData | Reading Ct values from qPCR experiments data into a qPCRset
sampleNames,qPCRset-method | Class "qPCRset"
sampleNames<-,qPCRset,character-method | Class "qPCRset"
setCategory | Assign categories to Ct values from qPCR data.
show,qPCRset-method | Class "qPCRset"
summary,qPCRset-method | Class "qPCRset"
ttestCtData | Differentially expressed features with qPCR: t-test
[,qPCRset-method | Class "qPCRset"