Package: RChASM
Title: Detection of Chromosomal Aneuploidies in Ancient DNA Studies
Version: 1.0.1
Authors@R: 
    c(
      person(
        given = "Adam B.", 
        family = "Rohrlach",
        email = "adam.rohrlach@adelaide.edu.au", 
        role = c("aut", "cph"),
        comment = c(ORCID = "0000-0002-4204-5018")
      ), 
    person(
      given = "Jono", 
      family = "Tuke", 
      email = "simon.tuke@adelaide.edu.au", 
      role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-1688-8951")
    ), 
    person(
      given = "Wolfgang", 
      family = "Haak",
      email = "wolfgang_haak@eva.mpg.de", 
      role = "aut",
      comment = c(ORCID = "0000-0003-2475-2007")
    )
    )
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).
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports: checkmate, cowplot, dplyr, EnvStats, ggplot2, ggrepel, ggsci,
        ggstar, magrittr, matrixStats, mclust, rstatix, sirt, stringr,
        tibble, tidyr, readr
LazyData: true
Suggests: knitr, rmarkdown, extraDistr
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
URL: https://jonotuke.github.io/RChASM/,
        https://github.com/jonotuke/RChASM
BugReports: https://github.com/jonotuke/RChASM/issues
NeedsCompilation: no
Packaged: 2026-04-22 07:52:48 UTC; a1078881
Author: Adam B. Rohrlach [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-4204-5018>),
  Jono Tuke [aut, cre] (ORCID: <https://orcid.org/0000-0002-1688-8951>),
  Wolfgang Haak [aut] (ORCID: <https://orcid.org/0000-0003-2475-2007>)
Maintainer: Jono Tuke <simon.tuke@adelaide.edu.au>
Repository: CRAN
Date/Publication: 2026-04-22 08:10:10 UTC
Built: R 4.4.3; ; 2026-04-22 09:15:30 UTC; unix
