Package: segtest 1.0.1

segtest: Tests for Segregation Distortion in Polyploids

Provides a suite of tests for segregation distortion in F1 polyploid populations (for now, just tetraploids). This is under different assumptions of meiosis. Details of these methods are described in Gerard et al. (2024) <doi:10.1101/2024.02.07.579361>. This material is based upon work supported by the National Science Foundation under Grant No. 2132247. The opinions, findings, and conclusions or recommendations expressed are those of the author and do not necessarily reflect the views of the National Science Foundation.

Authors:David Gerard [aut, cre], Mira Thakkar [aut], NSF DBI 2132247 [fnd]

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segtest.pdf |segtest.html✨
segtest/json (API)

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

Peer review:

Bug tracker:https://github.com/dcgerard/segtest/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ufit - Genotype data from Cappai et al.
  • ufit2 - Genotype data from Cappai et al.
  • ufit3 - Genotype data from Cappai et al.

On CRAN:

cpp

4.78 score 1 stars 3 scripts 130 downloads 27 exports 48 dependencies

Last updated 2 months agofrom:19f6d2ad23. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-win-x86_64OKDec 21 2024
R-4.5-linux-x86_64OKDec 21 2024
R-4.4-win-x86_64OKDec 21 2024
R-4.4-mac-x86_64OKDec 21 2024
R-4.4-mac-aarch64OKDec 21 2024
R-4.3-win-x86_64OKDec 21 2024
R-4.3-mac-x86_64OKDec 21 2024
R-4.3-mac-aarch64OKDec 21 2024

Exports:chisq_g4chisq_gl4em_ligcount_to_gvecgvec_to_gcountis_valid_2like_gknown_2like_gknown_3like_glpknown_2like_glpknown_3llike_lilrt_men_g4lrt_men_gl4multi_lrtmultidog_to_goffspring_genooffspring_gf_2offspring_gf_3otest_gpo_glpolymapr_testpvec_tet_2pvec_tet_3simf1gsimf1glsimglthree_to_two

Dependencies:assertthatclicodetoolscolorspacedigestdoFuturedoRNGfansifarverforeachfuturefuture.applyggplot2globalsgluegtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangrngtoolsscalesstringistringrtibbleupdogutf8vctrsviridisLitewithr

Introduction to segtest

Rendered fromintro.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2024-10-03
Started: 2024-08-29

Parallel Testing

Rendered fromparallel.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2024-10-18
Started: 2024-10-03

Readme and manuals

Help Manual

Help pageTopics
Chi Square test when genotypes are knownchisq_g4
Chi-Sq for GLchisq_gl4
EM algorithm from Li (2011)em_li
Converts genotype counts to genotype vectors.gcount_to_gvec
Inverse function of 'gcount_to_gvec()'.gvec_to_gcount
Tests if the two parameter model is validis_valid_2
Iterator over arrayiter.array
Likelihood under three parameter model when genotypes are knownlike_gknown_2
Likelihood under three parameter model when genotypes are knownlike_gknown_3
Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.like_glpknown_2
Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.like_glpknown_3
Objective function for 'em_li()'llike_li
Likelihood ratio test for segregation distortion with known genotypeslrt_men_g4
Likelihood ratio test using genotype likelihoods.lrt_men_gl4
Parallelized likelihood ratio test for segregation distortion.multi_lrt
Converts multidog output to a format usable for multi_lrt()multidog_to_g
Next element in an arraynextElem.arrayiter
Simulates genotypes given genotype frequencies.offspring_geno
Calculates offspring genotype frequencies under the two-parameter model.offspring_gf_2
Calculates offspring genotype frequencies under the three-parameter model.offspring_gf_3
Jointly tests for segregation distortion and number of incompatible genotypesotest_g
Generate genotype likelihoods from offspring genotypes.po_gl
Run segregation distortion tests as implemented in the polymapR package.polymapr_test
Tetraploid gamete frequencies of gametes when one parent's genotype is knownpvec_tet_2
Tetraploid gamete frequencies of gametes when one parent's genotype is knownpvec_tet_3
Simulate genotype counts from F1 individualssimf1g
Simulate genotype likelihoods of F1 individuals.simf1gl
Simulate genotype likelihoods from genotype countssimgl
Convert from three parameters to two parametersthree_to_two
Genotype data from Cappai et al. (2020)ufit ufit2 ufit3