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Package: polyBreedR 0.46

Jeffrey Endelman

polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Genomics-assisted breeding for polyploids (and diploids)

Authors:Jeffrey B. Endelman

polyBreedR_0.46.tar.gz
polyBreedR_0.46.zip(r-4.5)polyBreedR_0.46.zip(r-4.4)polyBreedR_0.46.zip(r-4.3)
polyBreedR_0.46.tgz(r-4.4-any)polyBreedR_0.46.tgz(r-4.3-any)
polyBreedR_0.46.tar.gz(r-4.5-noble)polyBreedR_0.46.tar.gz(r-4.4-noble)
polyBreedR_0.46.tgz(r-4.4-emscripten)polyBreedR_0.46.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

On CRAN:

3.74 score 10 stars 6 scripts 21 exports 70 dependencies

Last updated 3 months agofrom:85c9b549a6. Checks:ERROR: 1 WARNING: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 28 2024
R-4.5-win	WARNING	Nov 28 2024
R-4.5-linux	WARNING	Nov 28 2024
R-4.4-win	WARNING	Nov 28 2024
R-4.4-mac	WARNING	Nov 28 2024
R-4.3-win	WARNING	Nov 28 2024
R-4.3-mac	WARNING	Nov 28 2024

Exports:A_mat ADsplit array2vcf check_ploidy check_trio dart2vcf G_mat gbs geno_call get_pedigree GT2DS GvsA impute impute_L2H impute_LA madc merge_impute readXY update_alias vcf2csv write_vcf

Dependencies:AGHmatrix ape assertthat cli cluster codetools colorspace cpp11 data.table digest doFuture doRNG dplyr fansi farver foreach future future.apply generics ggplot2 ggrepel globals glue gtable HaploSim isoband iterators labeling lattice lifecycle listenv magrittr MASS Matrix memuse mgcv munsell nlme parallelly pedigree permute pillar pinfsc50 pkgconfig plyr purrr R6 randomForest RColorBrewer Rcpp RcppArmadillo reshape reshape2 rlang rngtools rrBLUP scales stringi stringr tibble tidyr tidyselect updog utf8 vcfR vctrs vegan viridisLite withr zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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