Package: qtlDesign 0.953

qtlDesign: Design of QTL (Quantitative Trait Locus) Experiments

Design of QTL (quantitative trait locus) experiments involves choosing which strains to cross, the type of cross, genotyping strategies, phenotyping strategies, and the number of progeny to raise and phenotype. This package provides tools to help make such choices. Sen and others (2007) <doi:10.1007/s00335-006-0090-y>.

Authors:Saunak Sen [aut, cre], Jaya Satagopan [ctb], Karl Broman [ctb], Gary Churchill [ctb], Brian Yandell [ctb]

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qtlDesign.pdf |qtlDesign.html
qtlDesign/json (API)

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

Peer review:

On CRAN:

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

21 exports 1 stars 1.58 score 0 dependencies 5 mentions 31 scripts 256 downloads

Last updated 5 months agofrom:3e3843397b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winOKSep 14 2024
R-4.5-linuxOKSep 14 2024
R-4.4-winOKSep 14 2024
R-4.4-macOKSep 14 2024
R-4.3-winOKSep 14 2024
R-4.3-macOKSep 14 2024

Exports:ci.lengthdeflatedetectableerror.vargenetic.distgmeans2effectinfoinfo2costmmanunullinfooptselectionoptspacingpowercalcprop.varrecombsamplesizetailprobtauthreshversion.qtlDesign

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Calculating expected QTL confidence interval widthsci.length
Information under null hypothesis of equal meansdeflate deflate.bc deflate.f2 info info.bc info.f2 nullinfo
Functions to calculate information-cost ratiosinfo2cost info2cost.bc info2cost.f2
Calculate scores for minimum moment abberations.eff1 K1 K12 Kstat
Selective phenotyping with similarity measure 2mma
MMA utilitymma.level
Optimal marker spacingoptspacing optspacing.bc optspacing.f2
Optimal selection fractionoptselection optselection.bc optselection.f2
Version of qtlDesign packageversion.qtlDesign
Power, sample size, and detectable effect size calculationsdetectable detectable.bc detectable.f2 detectable.ri powercalc powercalc.bc powercalc.f2 powercalc.ri samplesize samplesize.bc samplesize.f2 samplesize.ri
Calculating thresholds and tail probabilities for genome scanstailprob thresh
Utility functionsgenetic.dist recomb
Effect size, proportion variance explained, and error variance calculationserror.var gmeans2effect prop.var