/precision-clonality-code

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

Primary LanguageR

PRECISION clonality paper

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

Directory structure

  • breakclone - R package to assess clonality of tumour pairs.
  • analysis - Scripts used in the analysis.

Analysis

This directory contains the following scripts used in the analysis:

Copy Number analysis related scripts:

  • 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.

Panel-seq analysis related scripts:

  • 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 related scripts:

  • wes_analysis.R takes as an input table of mutations and outputs WES data analysis and plots VAF scatterplots, VAF boxplots and oncoPrint.