breakclone R package and scripts used in the analysis performed for the PRECISION clonality paper.

• breakclone - R package to assess clonality of tumour pairs.
• analysis - Scripts used in the analysis.
• precision_clonality - Link to Platypus and WES scripts.
• PRECISION_clonality_sc - Link to scDNA script.

This directory contains the following scripts used in the analysis:

• plotSegs.R R function which takes as an input a QDNAseq object and plots the copy number profile of an specific sample.
• exportSharedBreaks.R R function which takes as an input a segment table generated by the breakclone::readAlleleSpecific or breakclone::readVCFCn functions and exports shared breakpoints for a pair of samples.
• plotClonality.R R function which takes as an input directory to shared breakpoints exported by exportSharedBreaks.R, a segment table generated by the breakclone::readAlleleSpecific or breakclone::readVCFCn functions and additional details for each sample (relatedness verdict, clonality score...) and plots a stacked barplot of total, shared and non-shared breakpoints and breakclone score per sample for copy number data.
• HeatmapCNPairs.R R function which takes as an input directory to shared breakpoints exported by exportSharedBreaks.R and a call score copy number matrix for a pair of samples and plots a copy number heatmap with shared breakpoints and copy number bar.

• make_oncoPrint.R takes as an input table of mutations and outputs statistical analysis of number of mutations for all genes in the panel and plots oncoPrint.

• wes_analysis.R takes as an input table of mutations and outputs WES data analysis and plots VAF scatterplots, VAF boxplots and oncoPrint.
• wes_pipe.sh located in the linked submodule precision_clonality. Command in the pipeline script to generate platyPus. Platypus 0.5.2 was used to call germline variants.

• scDNA.R processes scDNA data. Located in navinlabcode\PRECISION_clonality_sc linked submodule.