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Package: diaQTL 1.13

Jeffrey Endelman

diaQTL: QTL Analysis in Diallel Populations

QTL analysis of diploid and autotetraploid diallel populations. Phenotypes are regressed on genotype probabilities, and the regression coefficients are random effects.

Authors:Jeffrey B. Endelman and Rodrigo R. Amadeu

diaQTL_1.13.tar.gz
diaQTL_1.13.zip(r-4.7-any)diaQTL_1.13.zip(r-4.6-any)diaQTL_1.13.zip(r-4.5-any)
diaQTL_1.13.tgz(r-4.6-any)diaQTL_1.13.tgz(r-4.5-any)
diaQTL_1.13.tar.gz(r-4.7-any)diaQTL_1.13.tar.gz(r-4.6-any)
diaQTL_1.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
diaQTL/json (API)

# Install 'diaQTL' in R:

install.packages('diaQTL', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jendelman/diaqtl/issues

Datasets:

F1codes - Genotype codes for F1 populations
S1codes - Genotype codes for S1 populations

On CRAN:

4.59 score 13 stars 7 scripts 25 exports 55 dependencies

Last updated from:9526a6d991. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel	OK	172
source / vignettes	OK	635
linux-release	OK	147
macos-release	OK	143
macos-oldrel	OK	110
windows-devel	OK	121
windows-release	OK	115
windows-oldrel	OK	116
wasm-release	OK	122

Exports:BayesCI convert_mappoly convert_onemap convert_polyorigin convert_rabbit diallel_geno diallel_geno_pheno DIC_thresh diplo_freq diplo_get fine_map fitQTL get_map haplo_cluster haplo_freq haplo_get haplo_match haplo_plot IBDmat phased_parents read_data scan1 scan1_permute scan1_summary set_params

Dependencies:arrangements BGLR cli coda commonmark cpp11 curl dplyr farver generics ggdendro ggfittext ggplot2 glue gmp gridtext gtable isoband jpeg labeling lattice lifecycle litedown magrittr markdown MASS Matrix mgcv nlme pillar pkgconfig plyr png purrr R6 RColorBrewer Rcpp reshape2 rlang S7 scales scam shades stringi stringr tibble tidyr tidyselect truncnorm utf8 vctrs viridisLite withr xfun xml2

diaQTL Vignette

Rendered fromdiaQTL_vignette.Rmdusingknitr::rmarkdown

Last update: 2021-06-01
Started: 2021-04-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bayesian Credible Interval for QTL position	BayesCI
Generate diaQTL input files from MAPpoly	convert_mappoly
Generate diaQTL input files from OneMap	convert_onemap
Create diaQTL input files from PolyOrigin output	convert_polyorigin
Generate diaQTL input files from RABBIT MagicReconstruct	convert_rabbit
S4 class with genotype and phenotype data	diallel_geno_pheno diallel_geno_pheno-class
S4 class with genotype data	diallel_geno diallel_geno-class
delta DIC thresholds for scan1	DIC_thresh
Diplotype frequencies	diplo_freq
Dosage of parental diplotypes	diplo_get
Genotype codes for F1 populations	F1codes
Visualize haplotype switches for fine mapping	fine_map
Fit multiple QTL model	fitQTL
Get map summary from diallel_geno object	get_map
Cluster parental haplotypes	haplo_cluster
Haplotype frequencies	haplo_freq
Dosage of parental haplotypes	haplo_get
Match up parental haplotypes	haplo_match
Plot parental haplotype dosage	haplo_plot
Realized IBD relationship	IBDmat
Visualize phased SNPs of parents	phased_parents
Read data files	read_data
Genotype codes for S1 populations	S1codes
Single QTL scan	scan1
Permutation test for scan1	scan1_permute
Summary of scan1 result	scan1_summary
Determine number of iterations for MCMC	set_params