# Functions used to analyze early tumor evolution from whole genome sequencing data

## Documentation for package ‘LACHESIS’ version 1.1.1

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

## Help Pages

classifyLACHESIS | Classify a tumor's start of clonal outgrowth during tumorigenesis as "Early MRCA" or "Late MRCA" (favorable/ unfavorable prognosis) depending on the mutation density at its MRCA
clonalMutationCounter | Count clonal mutations on one or several chromosomal copies
estimateClonality | Assigning clonality status to every SNV
estimateMutationRate | Estimate the mutation rate from a cohort of tumors with age information
LACHESIS | Run MRCA density estimation for a set of tumors
MRCA | Compute mutation densities at ECA and MRCA
nbImport | Combine CNVs and SNVs
normalizeCounts | Normalize clonal mutation counts
plotClinicalCorrelations | Correlate SNV density at ECA/MRCA with clinical parameters such as age, OS, etc.
plotClonality | Plotting assigned clonality status for every SNV by chromosome
plotDiseaseTrajectories | Plot the disease trajectories in a cohort.
plotLachesis | Plot SNV densities at ECA and MRCA
plotMutationDensities | Plot normalized mutation density at copy number gain and MRCA per segment
plotNB | Plot VAF distribution per copy number
plotSurvival | Correlate SNV density timing at MRCA with Survival
plotVAFdistr | Plot histogram of VAF distribution
readCNV | Converts a user-specified bed-file with copy number information into a standardized format that can be used as input for downstream analysis
readVCF | Import a VCF file and extract read count