Package: bexy 0.1.3

Madleina Caduff

bexy: Visualize and Parse the Output of 'BeXY'

Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.

Authors:Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph Leuenberger [ctb], Daniel Wegmann [aut]

bexy_0.1.3.tar.gz
bexy_0.1.3.tar.gz(r-4.5-noble)bexy_0.1.3.tar.gz(r-4.4-noble)
bexy_0.1.3.tgz(r-4.4-emscripten)bexy_0.1.3.tgz(r-4.3-emscripten)
bexy.pdf |bexy.html✨
bexy/json (API)
NEWS

# Install 'bexy' in R:
install.packages('bexy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.30 score 224 downloads 21 exports 36 dependencies

Last updated 3 months agofrom:96d2546ca9. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-linuxOKNov 22 2024

Exports:bexygetPosteriorMeanRhogetPosteriorModeAutosomalTrisomygetPosteriorModeScaffoldTypesgetPosteriorModeSexKaryotypesgetSamplesWithAutosomalTrisomygetSamplesWithThisKaryotypegetScaffoldsWithThisTypeplot.bexyplotAutosomalTrisomyplotAutosomalTrisomyCountsplotAutosomalTrisomyPosteriorProbabilitiesplotBarsplotCountsplotMCMCTraceplotTernaryprint.bexysummary.bexywritePosteriorModeAutosomalTrisomieswritePosteriorModeScaffoldTypeswritePosteriorModeSexKaryotypes

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimePlotToolspromisesR6rappdirsRcppRcppHungarianrlangsassshinysourcetoolsspTeachingDemosTernarywithrxtable

Readme and manuals

Help Manual

Help pageTopics
Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing databexy
Getting posterior mean rho (ploidy ratio parameter) for each scaffoldgetPosteriorMeanRho
Getting the posterior mode for each autosomal trisomygetPosteriorModeAutosomalTrisomy
Getting the posterior mode for each scaffold typegetPosteriorModeScaffoldTypes
Getting the posterior mode for each sex karyotypegetPosteriorModeSexKaryotypes
Getting all samples classified as a certain autosomal trisomygetSamplesWithAutosomalTrisomy
Getting all samples classified as a specific sex karyotypegetSamplesWithThisKaryotype
Getting all scaffolds classified as a specific scaffold typegetScaffoldsWithThisType
Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).plot.bexy
Plotting the autosomal trisomiesplotAutosomalTrisomy
Plotting the autosomal trisomies: counts on that scaffoldplotAutosomalTrisomyCounts
Plotting the autosomal trisomies: posterior probabilitiesplotAutosomalTrisomyPosteriorProbabilities
Plotting a barplot with the posterior probabilities of each sex karyotype per sampleplotBars
Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotypeplotCounts
Plot the MCMC trace for a specific parameterplotMCMCTrace
Plotting the ternary of a bexy objectplotTernary
Printing a bexy objectprint.bexy
Summarizing a bexy objectsummary.bexy
Write a file with the posterior mode for each autosomal trisomywritePosteriorModeAutosomalTrisomies
Write a file with the posterior mode for each scaffold typewritePosteriorModeScaffoldTypes
Write a file with the posterior mode for each sex karyotypewritePosteriorModeSexKaryotypes