Package: QTL.gCIMapping 3.4

QTL.gCIMapping: QTL Genome-Wide Composite Interval Mapping

Conduct multiple quantitative trait loci (QTL) and QTL-by-environment interaction (QEI) mapping via ordinary or compressed variance component mixed models with random- or fixed QTL/QEI effects. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve or on each locus curve are viewed as potential main-effect QTLs and QEIs, all their effects are included in a multi-locus model, their effects are estimated by both least angle regression and empirical Bayes (or adaptive lasso) in backcross and F2 populations, and true QTLs and QEIs are identified by likelihood radio test. See Zhou et al. (2022) <doi:10.1093/bib/bbab596> and Wen et al. (2018) <doi:10.1093/bib/bby058>.

Authors:Zhou Ya-Hui, Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming

QTL.gCIMapping_3.4.tar.gz
QTL.gCIMapping_3.4.zip(r-4.5)QTL.gCIMapping_3.4.zip(r-4.4)QTL.gCIMapping_3.4.zip(r-4.3)
QTL.gCIMapping_3.4.tgz(r-4.4-x86_64)QTL.gCIMapping_3.4.tgz(r-4.4-arm64)QTL.gCIMapping_3.4.tgz(r-4.3-x86_64)QTL.gCIMapping_3.4.tgz(r-4.3-arm64)
QTL.gCIMapping_3.4.tar.gz(r-4.5-noble)QTL.gCIMapping_3.4.tar.gz(r-4.4-noble)
QTL.gCIMapping_3.4.tgz(r-4.4-emscripten)QTL.gCIMapping_3.4.tgz(r-4.3-emscripten)
QTL.gCIMapping.pdf |QTL.gCIMapping.html✨
QTL.gCIMapping/json (API)

# Install 'QTL.gCIMapping' in R:
install.packages('QTL.gCIMapping', repos = c('https://yuanmingzhang.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • DHdata - DH example data
  • F2data - F2 example data from 2 environments

On CRAN:

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

11 exports 1 stars 0.49 score 39 dependencies 1 dependents 2 scripts 439 downloads

Last updated 3 years agofrom:9a8f24338a. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-win-x86_64OKAug 22 2024
R-4.5-linux-x86_64OKAug 22 2024
R-4.4-win-x86_64OKAug 22 2024
R-4.4-mac-x86_64OKAug 22 2024
R-4.4-mac-aarch64OKAug 22 2024
R-4.3-win-x86_64OKAug 22 2024
R-4.3-mac-x86_64OKAug 22 2024
R-4.3-mac-aarch64OKAug 22 2024

Exports:DodatamarkerinsertQTL.gCIMappingReaddataWangFWangSWenFWenSZhouFZhouMethodZhouMethod_single_env

Dependencies:cellrangerclicodetoolscpp11crayondata.tabledoParallelfansiforeachglmnetgluehmsiteratorslarslatticelifecyclemagrittrMASSMatrixopenxlsxpillarpkgconfigprettyunitsprogressqtlR6RcppRcppEigenreadxlrematchrlangshapestringistringrsurvivaltibbleutf8vctrszip