Package: ldsep 2.1.5

ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.

Authors:David Gerard [aut, cre]

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

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

Peer review:

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • glike - Genotype log-likelihoods from 'uit'
  • gp - Posterior probabilities from 'uit'
  • uit - Updog fits on the data from Uitdewilligen et. al.

On CRAN:

5.13 score 8 stars 17 scripts 249 downloads 16 exports 33 dependencies

Last updated 2 years agofrom:cbd1df52b4. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 12 2024
R-4.5-win-x86_64NOTEOct 12 2024
R-4.5-linux-x86_64NOTEOct 12 2024
R-4.4-win-x86_64NOTEOct 12 2024
R-4.4-mac-x86_64NOTEOct 12 2024
R-4.4-mac-aarch64NOTEOct 12 2024
R-4.3-win-x86_64NOTEOct 12 2024
R-4.3-mac-x86_64NOTEOct 12 2024
R-4.3-mac-aarch64NOTEOct 12 2024

Exports:Dprimeformat_lddfget_prob_arraygl_to_gpis.lddfldestldest_compldest_hapldfastldshrinkmldestpbnorm_distpvcalcslcorsldestzshrink

Dependencies:abindashrclueclustercodetoolscorrplotdoParalleletrunctfBasicsforeachgssinvgammairlbaiteratorslatticelpSolveMASSMatrixmatrixStatsmixsqpmodeestRcppRcppArmadillormutilrpartspatialSQUAREMstablestablediststatiptimeDatetimeSeriestruncnorm

Fast LD Estimation

David Gerard

Rendered fromfast.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2021-09-28
Started: 2020-09-14

LD Estimation Pipeline from VCF

Rendered fromvcf.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2022-02-09
Started: 2020-10-23