RChASM - Detection of Chromosomal Aneuploidies in Ancient DNA Studies
An R implementation of ChASM (Chromosomal Aneuploidy
Screening Methodology): a statistically rigorous Bayesian
approach for screening data sets for autosomal and sex
chromosomal aneuploidies. This package 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, This package
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). This package 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).
