Package: LACHESIS 1.1.0

Installation | Citation | Input Data | Copy Number Variation (CNV) File | Single Nucleotide Variant (SNV) File | Package Output | Datatables (.txt) | Graphs (.pdf) | Structure | LACHESIS Main Workflow | Importing Data | Importing Copy Number Information (readCNV) | Handling Missing Allele Information | Input | Output | Example using output from ACESeq as copy number information | Example using output from ASCAT as copy number information | Example using output from PURPLE as copy number information | Importing Variant Information (readVCF) | Example: SNV calls obtained with Mutect | Example: SNV calls obtained with Strelka | Example: SNV calls obtained with the dkfz SNV calling workflow | Plotting Variant Allele Frequencies (plotVAFdistr) | Example | Assigning copy number states to single nucleotide variants (nbImport) | Assignment of mutational signatures | Example using all variants from vcf file | Example using variants associated with specific SBS mutational signatures from vcf file | Plotting Imported Data (plotNB) | Example using variants assosciated with specific SBS mutational signatures from vcf file | Processing Clonal Mutations | Counting Clonal Mutations (ClonalMutationalCounter) | Normalizing Clonal Mutation Counts (normalizeCounts) | Inferring Clonal Evolution | Estimating Mutation Densities at ECA/MRCA (MRCA) | Input Parameters | Plotting Mutation Densities (plotMutationalDensities) | Estimating Clonality per SNV (estimateClonality) | Plotting Clonality per SNV (plotClonality) | LACHESIS Wrapper Function | Example with vectors | Example with tab-delimited sample-specification file | Example with multiple sample and data frame input | Plotting Cohort Analysis (plotLACHESIS) | Plotting Clinical Correlations (plotClinicalCorrelations) | Plotting Disease Trajectories (plotDiseaseTrajectories) | Plotting Survival (plotSurvival) | Classifying Tumor Evolution (classifyLACHESIS) | Quality control/ Filtering | Hypermutants | Ploidy and purity | VAF distribution | Positive Example | Negative Example | Warning Messages | readCNV | nbImport | MRCA | LACHESIS | plotLachesis | plotLachesis, plotClinicalCorrelations, plotSurvival | plotSurvival | How To Get Help | Session Info