Package: clipp 1.1.1

clipp: Calculating Likelihoods by Pedigree Paring

A fast and general implementation of the Elston-Stewart algorithm that can calculate the likelihoods of large and complex pedigrees. References for the Elston-Stewart algorithm are Elston & Stewart (1971) <doi:10.1159/000152448>, Lange & Elston (1975) <doi:10.1159/000152714> and Cannings et al. (1978) <doi:10.2307/1426718>.

Authors:James Dowty [aut, cre], Kevin Wong [aut]

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clipp_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
clipp/json (API)

# Install 'clipp' in R:

install.packages('clipp', repos = c('https://jgdowty.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

dat_large - Simulated data on one family with approximately 10,000 members
dat_small - Simulated data on 10 families with approximately 100 members each
penet_large - A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes
penet_small - A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes

On CRAN:

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

2.48 score 1 packages 5 scripts 302 downloads 9 exports 0 dependencies

Last updated from:43c693b066. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	109
source / vignettes	OK	172
linux-release-x86_64	OK	111
macos-release-arm64	OK	123
macos-oldrel-arm64	OK	152
windows-devel	OK	75
windows-release	OK	67
windows-oldrel	OK	72
wasm-release	OK	89

Exports:combine_loci geno_freq_monogenic geno_freq_phased geno_freq_polygenic genotype_probabilities pedigree_loglikelihood trans_monogenic trans_phased trans_polygenic

Dependencies:

Vignette for clipp

Rendered fromusing_clipp.Rmdusingknitr::rmarkdown

Last update: 2022-07-12
Started: 2022-07-12

Citation

Readme and manuals

Help Manual

Help page	Topics
clipp: Calculate Likelihoods by Pedigree Paring	clipp-package clipp
Combine the genotype frequencies and transition matrices of two genetic loci	combine_loci
Simulated data on one family with approximately 10,000 members	dat_large
Simulated data on 10 families with approximately 100 members each	dat_small
Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium	geno_freq_monogenic
Calculate phased genotype frequencies from allele frequencies, assuming Hardy-Weinberg equilibrium	geno_freq_phased
Genotype frequencies for the hypergeometric polygenic model	geno_freq_polygenic
Calculate genotype probabilities for a target person	genotype_probabilities
Calculate the log-likelihoods of pedigrees	pedigree_loglikelihood
A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes	penet_large
A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes	penet_small
The transmission matrix for a single genetic locus	trans_monogenic
The transmission matrix for phased genotypes	trans_phased
The transmission matrix for the hypergeometric polygenic model	trans_polygenic

Package: clipp 1.1.1

clipp: Calculating Likelihoods by Pedigree Paring

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)