Analysis of scDNA-seq data


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Documentation for package ‘scafari’ version 0.99.12

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scafari-package scafari: analyzing scDNA-seq data
annotateAmplicons Function: annotateAmplicons This function takes a SingleCellExperiment object as input and annotates the stored amplicons.
annotateVariants Function: annotateVariants This function takes a SingleCellExperiment object as input and performs variant annotation.
clusterVariantSelection Function: clusterVariantSelection This function takes selected variants and performs clustering on them.
filterVariants Function: filterVariants -- This function takes a SingleCellExperiment object as input and performs variant filtering
h5ToSce Function: h5ToSce This function takes the path of an h5 file and reads this into an object of the SingleCellExperiment class.
launchScafariShiny Launch Scafari Shiny Application
logLogPlot Plot a log-log plot for read counts
normalizeReadCounts This function normalizes the read counts contained within a 'SingleCellExperiment' object.
plotAmpliconDistribution Plot Distribution of Amplicons
plotClusterGenotype Plot Genotype Clusters
plotClusterVAF plot Cluster VAF This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest.
plotClusterVAFMap plot Cluster VAF Map This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest with clusters in the background.
plotElbow This function takes a SingleCellExperiment object and variants of interest as input and plots an elbow plot to perform k-means later.
plotGenotypequalityPerGenotype Plot Genotype Quality per Genotype
plotNormalizedReadCounts Plot normalized read counts
plotPanelUniformity Plot Panel Uniformity
plotVariantHeatmap Plot Variant Heatmap
scafari scafari: analyzing scDNA-seq data