R: Detection of Chromosomal Aneuploidies in Ancient DNA Studies

# Detection of Chromosomal Aneuploidies in Ancient DNA Studies

## Documentation for package ‘RChASM’ version 1.0.1

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

## 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