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RChASM: A Statistically Rigorous Method for the Detection of Chromosomal Aneuploidies in Ancient DNA Studies.
RChASM is an R implementation of ChASM (Chromosomal Aneuploidy Screening Methodology): a statistically rigorous Bayesian approach for screening data sets for autosomal and sex chromosomal aneuploidies. RChASM takes as input the number of (deduplicated) reads mapping to chromosomes 1-22 and the X and Y chromosomes, and models these using a Dirichlet-multinomial distribution. From this, RChASM returns posterior probabilities of sex chromosomal karyotypes (XX, XY, XXY, XYY, XXX and X) and full autosomal aneuploidies (trisomy 13, trisomy 18 and trisomy 21). RChASM also returns two diagnostic statistics: (i) a posterior probability addressing whether contamination between XX and XY may explain the observed sex chromosomal aneuploidy, and (ii) a chi-squared statistic measuring whether the observed read counts are too divergent from the underlying distribution (and may represent abnormal sequencing/quality issues).
You can install the development version of RChASM from GitHub with:
# install.packages("pak")
pak::pak("jonotuke/RChASM")Please see vignette("example_analysis") for a
tutorial
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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