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RChASM  

Detection of Chromosomal Aneuploidies in Ancient DNA Studies
View on CRAN: Click here


Download and install RChASM package within the R console
Install from CRAN:
install.packages("RChASM")

Install from Github:
library("remotes")
install_github("cran/RChASM")

Install by package version:
library("remotes")
install_version("RChASM", "1.0.0")



Attach the package and use:
library("RChASM")
Maintained by
Jono Tuke
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-03-03
Latest Update: 2026-03-03
Description:
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).
How to cite:
Jono Tuke (2026). RChASM: Detection of Chromosomal Aneuploidies in Ancient DNA Studies. R package version 1.0.0, https://cran.r-project.org/web/packages/RChASM. Accessed 25 Jun. 2026.
Previous versions and publish date:
1.0.0 (2026-03-03 22:20)
Other packages that cited RChASM R package
View RChASM citation profile
Other R packages that RChASM depends, imports, suggests or enhances
Complete documentation for RChASM
Functions, R codes and Examples using the RChASM R package
Full RChASM package functions and examples
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