Detection of Chromosomal Aneuploidies in Ancient DNA Studies

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Documentation for package ‘RChASM’ version 1.0.0

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

Help Pages

adjustA	Adjusts alpha vector for contamination karyotypes
bound	bounds number to be in [0,1] (contamination estimation)
callKaryotypes	Take prior and observed counts and calls karyotypes and Z-scores
combineData	combine data
ddirichletultinomial	calculate Dirichlet probabilities with filtering
dirichlet.mle_filter	calculate Dirichlet parameters with filtering
estimateGamma	Estimate contamination from XX and XY based on observed counts
example_data	example_data
filterOutliers	filter for outliers
makeC	make c vector for new karyotypes
makeDirichlet	function to make a Dirichlet prior
makeZscores	Calculates Z-scores per chromosome
plot_diagnostic	Plots diagnostic plots
printChASM	A function to print the result of the combined analysis to screen
processReadCounts	processReadCounts
runChASM	Title
saveChASM	A function for saving the results of a ChASM analysis as a tsv
summary_calls	summary_calls