Automated analysis of qPCR data


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Documentation for package ‘HTqPCR’ version 1.0.0

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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"