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

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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