Package: polyBreedR 0.45
Jeffrey Endelman
polyBreedR: Genomics-assisted breeding for polyploids (and diploids)
Genomics-assisted breeding for polyploids (and diploids)
Authors:
polyBreedR_0.45.tar.gz
polyBreedR_0.45.zip(r-4.5)polyBreedR_0.45.zip(r-4.4)polyBreedR_0.45.zip(r-4.3)
polyBreedR_0.45.tgz(r-4.4-any)polyBreedR_0.45.tgz(r-4.3-any)
polyBreedR_0.45.tar.gz(r-4.5-noble)polyBreedR_0.45.tar.gz(r-4.4-noble)
polyBreedR_0.45.tgz(r-4.4-emscripten)polyBreedR_0.45.tgz(r-4.3-emscripten)
polyBreedR.pdf |polyBreedR.html✨
polyBreedR/json (API)
NEWS
| # Install 'polyBreedR' in R: |
| install.packages('polyBreedR', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jendelman/polybreedr/issues
Last updated 3 months agofrom:7a5a742f92. Checks:ERROR: 1 WARNING: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Aug 19 2024 |
| R-4.5-win | WARNING | Aug 19 2024 |
| R-4.5-linux | WARNING | Aug 19 2024 |
| R-4.4-win | WARNING | Aug 19 2024 |
| R-4.4-mac | WARNING | Aug 19 2024 |
| R-4.3-win | WARNING | Aug 19 2024 |
| R-4.3-mac | WARNING | Aug 19 2024 |
Exports:A_matADsplitarray2vcfcheck_ploidycheck_triodart2vcfG_matgbsgeno_callget_pedigreeGT2DSGvsAimputeimpute_L2Himpute_LAmadcmerge_imputereadXYupdate_aliasvcf2csvwrite_vcf
Dependencies:AGHmatrixapeassertthatcliclustercodetoolscolorspacecpp11data.tabledigestdoFuturedoRNGdplyrfansifarverforeachfuturefuture.applygenericsggplot2ggrepelglobalsgluegtableHaploSimisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmemusemgcvmunsellnlmeparallellypedigreepermutepillarpinfsc50pkgconfigplyrpurrrR6randomForestRColorBrewerRcppRcppArmadilloreshapereshape2rlangrngtoolsrrBLUPscalesstringistringrtibbletidyrtidyselectupdogutf8vcfRvctrsveganviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Additive relationship matrix from pedigree | A_mat |
| Extract read counts from AD string | ADsplit |
| SNP array to VCF | array2vcf |
| Check ploidy for tetraploids | check_ploidy |
| Check markers for parent-offspring trio | check_trio |
| Convert DArTag to VCF | dart2vcf |
| Genomic relationship matrix | G_mat |
| Genotype calls for GBS | gbs |
| Genotype calls | geno_call |
| Generate pedigree | get_pedigree |
| Convert GT to ALT allele dosage (DS) | GT2DS |
| Plot G vs. A | GvsA |
| Impute missing data for bi-allelic markers | impute |
| Impute from low to high density markers by Random Forest | impute_L2H |
| Impute from low to high density markers by Linkage Analysis (LA) | impute_LA |
| Multi-Allelic Haplotype Counts for potato DArTag | madc |
| Merge two genotype matrices and impute missing data (deprecated) | merge_impute |
| Read SNP array intensity data | readXY |
| Update names based on alias | update_alias |
| Convert VCF to CSV | vcf2csv |
| Create VCFv4.3 file | write_vcf |
