Automated analysis of high-throughput qPCR data


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Documentation for package ‘HTqPCR’ version 1.12.0

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HTqPCR-package Analysis of High-Throughput qPCR data (HTqPCR)
.readCtBioMark Reading Ct values from qPCR experiments data into a qPCRset
.readCtCFX Reading Ct values from qPCR experiments data into a qPCRset
.readCtLightCycler Reading Ct values from qPCR experiments data into a qPCRset
.readCtOpenArray Reading Ct values from qPCR experiments data into a qPCRset
.readCtPlain Reading Ct values from qPCR experiments data into a qPCRset
.readCtSDS Reading Ct values from qPCR experiments data into a qPCRset
cbind Combine qPCRset objects
cbind.qPCRset Combine qPCRset objects
changeCtLayout Changing the dimensions (rows x columns) of qPCRset objects
clusterCt Clustering of qPCR Ct values
exprs-method Class "qPCRset"
exprs<--method Class "qPCRset"
featureCategory Class "qPCRset"
featureCategory-method Class "qPCRset"
featureCategory<- Class "qPCRset"
featureCategory<--method Class "qPCRset"
featureClass Class "qPCRset"
featureClass-method Class "qPCRset"
featureClass<- Class "qPCRset"
featureClass<--method Class "qPCRset"
featureNames-method Class "qPCRset"
featureNames<--method Class "qPCRset"
featurePos Class "qPCRset"
featurePos-method Class "qPCRset"
featurePos<- Class "qPCRset"
featurePos<--method Class "qPCRset"
featureType Class "qPCRset"
featureType-method Class "qPCRset"
featureType<- Class "qPCRset"
featureType<--method Class "qPCRset"
filterCategory Filter Ct values based on their feature categories.
filterCtData Filter out features (genes) from qPCR data.
flag Class "qPCRset"
flag-method Class "qPCRset"
flag<- Class "qPCRset"
flag<--method Class "qPCRset"
getCt Class "qPCRset"
getCtHistory 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
mannwhitneyCtData Differentially expressed features with qPCR: Mann-Whitney
n.samples Class "qPCRset"
n.wells Class "qPCRset"
normalizeCtData Normalization of Ct values from qPCR data.
plotCtArray Image plot of qPCR Ct values from an array format
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.
plotCtVariation Plot variation in Ct values across replicates
plotCVBoxes Boxplots of CV for qPCR Ct values.
qPCRpros Example processed qPCR data
qPCRraw Example raw qPCR data.
qPCRset-class Class "qPCRset"
rbind Combine qPCRset objects
rbind.qPCRset Combine qPCRset objects
readCtData Reading Ct values from qPCR experiments data into a qPCRset
sampleNames-method Class "qPCRset"
sampleNames<--method Class "qPCRset"
setCategory Assign categories to Ct values from qPCR data.
setCt<- Class "qPCRset"
setCtHistory<- Class "qPCRset"
show-method Class "qPCRset"
summary-method Class "qPCRset"
ttestCtData Differentially expressed features with qPCR: t-test
[-method Class "qPCRset"