Introduction | Install | Input data | Pedigree cleaning | Pedigree validation | Parentage assignment | Filling in missing parents of a pedigree | Breed and line composition | Complete workflow | Session information | How to cite | Acknowledgments
Package: BIGpopA 2.2.0
Josue Chinchilla-Vargas
BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids
Tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. 'BIGpopA' provides functions to check and correct common pedigree errors, assign parentage from SNP genotype data using Mendelian error rates, validate parent-offspring trios, and estimate genome-wide breed or line composition using quadratic programming. Pedigree validation and parentage assignment support any ploidy, using a polysomic Mendelian test for even ploidy and a homozygosity-based check for odd ploidy. Genotypes can be supplied as dosage tables, VCF files, or 'PLINK' .ped files. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>.
Authors:
BIGpopA_2.2.0.tar.gz
BIGpopA_2.2.0.zip(r-4.7-any)BIGpopA_2.2.0.zip(r-4.6-any)BIGpopA_2.2.0.zip(r-4.5-any)
BIGpopA_2.2.0.tgz(r-4.6-any)BIGpopA_2.2.0.tgz(r-4.5-any)
BIGpopA_2.2.0.tar.gz(r-4.7-any)BIGpopA_2.2.0.tar.gz(r-4.6-any)
BIGpopA_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BIGpopA/json (API)
| # Install 'BIGpopA' in R: |
| install.packages('BIGpopA', repos = c('https://breeding-insight.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/breeding-insight/bigpopa/issues
Last updated from:ca36034f20. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 172 | ||
| source / vignettes | OK | 208 | ||
| linux-release | OK | 156 | ||
| macos-release | OK | 107 | ||
| macos-oldrel | OK | 135 | ||
| windows-devel | OK | 114 | ||
| windows-release | OK | 129 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 107 |
Exports:allele_freq_polyassign_composition_linecheck_pedfind_parentageped_to_dosagesolve_composition_polyvalidate_pedigreevcf_to_dosage
Dependencies:clicpp11data.tabledplyrfarvergenericsggplot2gluegtablehmsisobandjanitorlabelinglifecyclelubridatemagrittrpillarpkgconfigpurrrquadprogR6RColorBrewerrlangS7scalessnakecasestringistringrtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute Allele Frequencies for Populations | allele_freq_poly |
| Assign Each Sample to a Reference Line | assign_composition_line |
| Check and Correct Common Pedigree Errors | check_ped |
| Find Parentage Assignments for Progeny | find_parentage |
| Convert a PLINK .ped File to a BIGpopA Genotype Matrix | ped_to_dosage |
| Compute Genome-Wide Breed Composition | solve_composition_poly |
| Validate Pedigree Trios Using Mendelian Error Analysis | validate_pedigree |
| Convert a VCF File to a BIGpopA Genotype Matrix | vcf_to_dosage |