Package: statgenMPP 1.0.3

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://bartjanvanrossum.r-universe.dev', 'https://cloud.r-project.org'))

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:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 10 scripts 602 downloads 5 exports 56 dependencies

Last updated 25 days agofrom:f8c45ac27c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024
R-4.4-win	OK	Nov 19 2024
R-4.4-mac	OK	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

Exports:calcIBDMPP createGDataMPP kinshipIBD readRABBITMPP selQTLMPP

Dependencies:agridat class classInt cli codetools colorspace crayon data.table DBI dotCall64 e1071 fansi farver foreach ggplot2 glue gridExtra gtable isoband iterators KernSmooth labeling lattice lifecycle LMMsolver magrittr maps MASS Matrix mgcv munsell nlme pillar pkgconfig proxy R6 RColorBrewer Rcpp RcppArmadillo RcppProgress rlang s2 scales sf sommer spam statgenGWAS statgenIBD stringi tibble units utf8 vctrs viridisLite withr wk

QTL Mapping in Multi-Parent Populations

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

Rendered fromQTLMapping_in_MultiParentPopulations.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-10-29
Started: 2022-03-21

Citation

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