# Analysis of scDNA-seq data

## Documentation for package ‘scafari’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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