Analysis of scDNA-seq data

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Documentation for package ‘scafari’ version 0.99.12

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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