Package: diemr 1.4.1
diemr: Diagnostic Index Expectation Maximisation in R
Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Authors:
diemr_1.4.1.tar.gz
diemr_1.4.1.zip(r-4.5)diemr_1.4.1.zip(r-4.4)diemr_1.4.1.zip(r-4.3)
diemr_1.4.1.tgz(r-4.4-any)diemr_1.4.1.tgz(r-4.3-any)
diemr_1.4.1.tar.gz(r-4.5-noble)diemr_1.4.1.tar.gz(r-4.4-noble)
diemr_1.4.1.tgz(r-4.4-emscripten)diemr_1.4.1.tgz(r-4.3-emscripten)
diemr.pdf |diemr.html✨
diemr/json (API)
NEWS
| # Install 'diemr' in R: |
| install.packages('diemr', repos = c('https://nmartinkova.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stuartjebaird/diem/issues
Last updated 2 months agofrom:cc15aee92f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 23 2024 |
| R-4.5-win | OK | Nov 23 2024 |
| R-4.5-linux | OK | Nov 23 2024 |
| R-4.4-win | OK | Nov 23 2024 |
| R-4.4-mac | OK | Nov 23 2024 |
| R-4.3-win | OK | Nov 23 2024 |
| R-4.3-mac | OK | Nov 23 2024 |
Exports:CheckDiemFormatdiememPolariseimportPolarizedpHetErrOnStateCountplotDeFinettiplotMarkerAxisplotPolarizedrank2mapsmoothPolarizedGenotypessStateCountvcf2diem
Dependencies:apecliclusterdigestdplyrfansigenericsgluelatticelifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigR6Rcpprlangstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithrzoo
diemr: Diagnostic index expectation maximisation in R
Rendered fromdiemr-diagnostic-index-expecation-maximisation-in-r.Rmdusingknitr::rmarkdownon Nov 23 2024.Last update: 2024-09-24
Started: 2022-03-29
Importing data for genome polarisation
Rendered fromImporting-data-for-genome-polarisation.Rmdusingknitr::rmarkdownon Nov 23 2024.Last update: 2024-09-24
Started: 2023-03-21
Understanding genome polarisation output files
Rendered fromUnderstanding-genome-polarisation-output-files.Rmdusingknitr::rmarkdownon Nov 23 2024.Last update: 2024-09-24
Started: 2024-07-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dataset of Butterfly Genotypes | brenthis |
| diem input file checker | CheckDiemFormat |
| Diagnostic Index Expectation Maximisation | diem |
| Polarises a marker | emPolarise |
| Imports genomic data polarized according to the specification | importPolarized |
| Model of Diagnostic Marker Based on All Individual State Counts | ModelOfDiagnostic |
| Dataset of Modified Genotypes of Bats | myotis |
| Hybrid index, heterozygosity, error rate | pHetErrOnStateCount |
| Plot the De Finetti Diagram for Polarized Genotypes | plotDeFinetti |
| Add a Marker Axis with Chromosome Names to a Plot of Polarized Genotypes | plotMarkerAxis |
| Plot Polarized Genotypes | plotPolarized |
| Convert SNP Ranks To Windows Corresponding to Mapping Distance | rank2map |
| Smooths Polarized Genotype States | smoothPolarizedGenotypes |
| Count states in a vector | sStateCount |
| Dataset of Fish Genotypes | testdata |
| Convert vcf files to diem format | vcf2diem |
