Package: statgenMPP 1.0.4

Bart-Jan van Rossum

statgenMPP: QTL Mapping for Multi Parent Populations

For Multi Parent Populations (MPP) Identity By Descend (IBD) probabilities are computed using Hidden Markov Models. These probabilities are then used in a mixed model approach for QTL Mapping as described in Li et al. (<doi:10.1007/s00122-021-03919-7>).

Authors:Martin Boer [aut], Wenhao Li [aut], Bart-Jan van Rossum [aut, cre], Fred van Eeuwijk [ctb]

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statgenMPP.pdf |statgenMPP.html✨
statgenMPP/json (API)
NEWS

# Install 'statgenMPP' in R:

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

Bug tracker:https://github.com/biometris/statgenmpp/issues

Datasets:

barleyMQM - Pre-computed MQM output barley
barleyPheno - Phenotypic data for awn length in barley
maizeMQM - Pre-computed MQM output maize
maizeSQM - Pre-computed SQM output maize

On CRAN:

genetics mpp qtl-mapping

4.94 score 11 scripts 629 downloads 5 exports 44 dependencies

Last updated 28 days agofrom:bc969fad50. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 12 2025
R-4.5-win	OK	Feb 12 2025
R-4.5-mac	OK	Feb 12 2025
R-4.5-linux	OK	Feb 12 2025
R-4.4-win	OK	Feb 12 2025
R-4.4-mac	OK	Feb 12 2025
R-4.3-win	OK	Feb 12 2025
R-4.3-mac	OK	Feb 12 2025

Exports:calcIBDMPP createGDataMPP kinshipIBD readRABBITMPP selQTLMPP

Dependencies:cli codetools colorspace crayon data.table dotCall64 fansi farver foreach ggplot2 glue gridExtra gtable isoband iterators labeling lattice lifecycle LMMsolver magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo RcppProgress rlang scales sommer spam statgenGWAS statgenIBD stringi tibble utf8 vctrs viridisLite withr

QTL Mapping in Multi-Parent Populations

Wenhao Li, Martin Boer, and Bart-Jan van Rossum

Rendered fromQTLMapping_in_MultiParentPopulations.Rmdusingknitr::rmarkdownon Feb 12 2025.

Last update: 2025-02-11
Started: 2022-03-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Pre-computed MQM output barley	barleyMQM
Phenotypic data for awn length in barley	barleyPheno
IBD calculation for multi parental populations	calcIBDMPP
Create an object of class gDataMPP	createGDataMPP
Compute kinship matrix for IBD probabilities	kinshipIBD
Pre-computed MQM output maize	maizeMQM
Pre-computed SQM output maize	maizeSQM
Plot function for the class 'gDataMPP'	plot.gDataMPP
Plot function for the class 'QTLMPP'	plot.QTLMPP
Print summary of object of class 'summary.QTLMPP'	print.summary.QTLMPP
Read IBD probabilities	readRABBITMPP
Multi round genome scans for QTL detection	selQTLMPP
Summary function for the class 'gDataMPP'	summary.gDataMPP
Summary function for the class 'QTLMPP'	summary.QTLMPP