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

## Documentation for package ‘LACHESIS’ version 0.99.4

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

## Help Pages

classifyLACHESIS | Classify a tumor's start of clonal outgrowth during tumorigenesis as "early" or "late" (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
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
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