Package: genogeographer 0.1.19
Torben Tvedebrink
genogeographer: Methods for Analysing Forensic Ancestry Informative Markers
Evaluates likelihood ratio tests for alleged ancestry. Implements the methods of Tvedebrink et al (2018) <doi:10.1016/j.tpb.2017.12.004>.
Authors:
genogeographer_0.1.19.tar.gz
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genogeographer.pdf |genogeographer.html✨
genogeographer/json (API)
| # Install 'genogeographer' in R: |
| install.packages('genogeographer', repos = c('https://tvedebrink.r-universe.dev', 'https://cloud.r-project.org')) |
- kidd_loci - Kenn Kidd Lab markers
- main_alleles - AIMs markers in Precision ID Ancestry Panel
- seldin_loci - Seldin Lab markers
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:fc4fa2236f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 21 2024 |
| R-4.5-win | OK | Aug 21 2024 |
| R-4.5-linux | OK | Aug 21 2024 |
| R-4.4-win | OK | Aug 21 2024 |
| R-4.4-mac | OK | Aug 21 2024 |
| R-4.3-win | OK | Aug 21 2024 |
| R-4.3-mac | OK | Aug 21 2024 |
Exports:app_genogeobar_colourerror_bar_plotexponent_tiltgenogeoLR_tablemap_plotpops_to_DBprofile_AA_x0profile_admixturerandom_AIMs_profilesimulate_pops
Dependencies:anytimebase64encBHbitbit64bslibcachemcellrangerclicliprcolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefansifarverfastmapfontawesomeforcatsforeignfsgenericsggplot2gluegtablehavenhighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclemagrittrmapsMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsrasterRColorBrewerRcppreadrreadxlrematchriorlangrmarkdownsassscalesshinyshinycssloadersshinyjsshinyWidgetssourcetoolsspstringistringrterratibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrwritexlxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Shiny application for GenoGeoGrapher | app_genogeo |
| bar_colour | bar_colour |
| Plot log likelihoods of profiles with approximate confidence intervals | error_bar_plot |
| P-values from Importing Sampling using Exponential tilting | exponent_tilt |
| Likelihood ratio tests for AIMs | genogeo |
| genogeographer: Methods for analysing forensic Ancestry Informative Markers | genogeographer-package genogeographer |
| Kenn Kidd Lab markers | kidd_loci |
| Compute pairwise likelihood ratios | LR_table |
| AIMs markers in Precision ID Ancestry Panel (Thermo Fisher Scientific) | main_alleles |
| Plot LTR z-scores on map | map_plot |
| Pre-compute the scores for a given reference database | pops_to_DB |
| Function that compute the genotype probability for each population (rows in df) | profile_AA_x0 |
| Compute the z-score (and more) for admixed hypotheses | profile_admixture |
| Simulate a random AIMs profile | random_AIMs_profile |
| Seldin Lab markers | seldin_loci |
| Simulate random populations | simulate_pops |