Introduction | Running the analysis using runChASM() | Interpreting results and producing diagnostic plots | Uncommon aneuploidies - analysis overview | Autosomal aneuploidies | Sex chromosomal aneuploidies | The limits of how samples can behave | Pre-processing your data using our script
Package: RChASM 1.0.1
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).
Authors:
RChASM_1.0.1.tar.gz
RChASM_1.0.1.zip(r-4.7-any)RChASM_1.0.1.zip(r-4.6-any)RChASM_1.0.1.zip(r-4.5-any)
RChASM_1.0.1.tgz(r-4.6-any)RChASM_1.0.1.tgz(r-4.5-any)
RChASM_1.0.1.tar.gz(r-4.7-any)RChASM_1.0.1.tar.gz(r-4.6-any)
RChASM_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RChASM/json (API)
| # Install 'RChASM' in R: |
| install.packages('RChASM', repos = c('https://jonotuke.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jonotuke/rchasm/issues
Pkgdown/docs site:https://jonotuke.github.io
Datasets:
- example_data - Example_data
Last updated from:6cf17e3582. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 166 | ||
| source / vignettes | OK | 223 | ||
| linux-release-x86_64 | OK | 160 | ||
| macos-release-arm64 | OK | 142 | ||
| macos-oldrel-arm64 | OK | 203 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 86 | ||
| windows-oldrel | OK | 109 | ||
| wasm-release | OK | 176 |
Exports:%>%plot_diagnosticprintChASMrunChASMsaveChASMsummary_calls
Dependencies:abindadmiscbackportsbase64encbitbit64bootbroombslibcachemcarcarDataCDMcheckmateclicliprcolorspacecorrplotcowplotcpp11crayonDerivdigestdoBydplyrEnvStatsevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastFormulafracdifffsgdtoolsgenericsggiraphggplot2ggrepelggsciggstargluegridExtragtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmclustmemoisemgcvmimeminqamodelrmvtnormnlmenloptrnnetnortestnumDerivpbapplypbkrtestpbvpillarpkgconfigpolycorprettyunitsprogresspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangrmarkdownrstatixS7sassscalessirtSparseMstringistringrsurvivalsystemfontsTAMtibbletidyrtidyselecttimeDatetinytextzdburcautf8vctrsviridisLitevroomwithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adjusts alpha vector for contamination karyotypes | adjustA |
| bounds number to be in [0,1] (contamination estimation) | bound |
| Take prior and observed counts and calls karyotypes and Z-scores | callKaryotypes |
| combine data | combineData |
| calculate Dirichlet probabilities with filtering | ddirichletultinomial |
| calculate Dirichlet parameters with filtering | dirichlet.mle_filter |
| Estimate contamination from XX and XY based on observed counts | estimateGamma |
| example_data | example_data |
| filter for outliers | filterOutliers |
| make c vector for new karyotypes | makeC |
| function to make a Dirichlet prior | makeDirichlet |
| Calculates Z-scores per chromosome | makeZscores |
| Plots diagnostic plots | plot_diagnostic |
| A function to print the result of the combined analysis to screen | printChASM |
| processReadCounts | processReadCounts |
| Title | runChASM |
| A function for saving the results of a ChASM analysis as a tsv | saveChASM |
| summary_calls | summary_calls |
