Package: purgeR 1.8.2

Eugenio López-Cortegano

purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.

Authors:Eugenio López-Cortegano [aut, cre]

purgeR_1.8.2.tar.gz
purgeR_1.8.2.tar.gz(r-4.5-noble)purgeR_1.8.2.tar.gz(r-4.4-noble)
purgeR_1.8.2.tgz(r-4.4-emscripten)purgeR_1.8.2.tgz(r-4.3-emscripten)
purgeR.pdf |purgeR.html✨
purgeR/json (API)
NEWS

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

Peer review:

Bug tracker:https://gitlab.com/elcortegano/purger

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • arrui - Arrui pedigree
  • atlas - Cuvier's gazelle pedigree
  • dama - Dama gazelle pedigree
  • darwin - Darwin/Wedgwood pedigree
  • dorcas - Dorcas gazelle pedigree

cpp

2.41 score 13 scripts 244 downloads 25 exports 18 dependencies

Last updated 1 years agofrom:724e6f6e15. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 23 2024
R-4.5-linux-x86_64OKDec 23 2024

Exports:exp_Fexp_Faexp_gip_Fip_Faip_Fijip_gip_opped_cleanped_graphped_maternalped_renameped_sortpop_hwdpop_Napop_Naepop_Nancestorspop_Nepop_Nfpop_Nfepop_Ngpop_tw_grandoffspringw_offspringw_reproductive_value

Dependencies:clicodetoolscrayondoSNOWforeachgluehmsiteratorslifecyclepkgconfigprettyunitsprogressR6RcppRcppProgressrlangsnowvctrs

Inbreeding and Purging Estimates

Eugenio López-Cortegano

Rendered fromip.Rmdusingknitr::rmarkdownon Dec 23 2024.

Last update: 2023-11-29
Started: 2021-04-30

purgeR tutorial

Eugenio López-Cortegano

Rendered frompurgeR-tutorial.Rmdusingknitr::rmarkdownon Dec 23 2024.

Last update: 2023-11-29
Started: 2021-04-30

Readme and manuals

Help Manual

Help pageTopics
Individuals to be evaluated in purging analysesancestors
Arrui pedigreearrui
Cuvier's gazelle pedigreeatlas
Check ancestor individualscheck_ancestors
Check basiccheck_basic
Check if a variable is boolean or notcheck_bool
Check that optional column is includedcheck_col
Check purging coefficientcheck_d
Check pedigree classcheck_df
Check columns with inbreeding valuescheck_Fcol
Check individual indexcheck_index
Check if a variable is a positive integer or notcheck_int
Check if a variable has length >1check_length
Check if a vector contains NA valuescheck_na
Check that mandatory column names are includedcheck_names
Check Necheck_Ne
Check if optional column is includedcheck_not_col
Check observed and expected number of rowscheck_nrows
Check individual ordercheck_order
Check columns with reference individualscheck_reference check_target
Check repeated idscheck_repeat_id
Check columns with generation numberscheck_tcol
Check that mandatory column names are of type intcheck_types
Check individuals named zerocheck_zero_id
Dama gazelle pedigreedama
Darwin/Wedgwood pedigreedarwin
Individual inbreeding variationdelta_Fi
Dorcas gazelle pedigreedorcas
Expected inbreeding coefficientexp_F
Expected ancestral inbreeding coefficientexp_Fa
Expected purged inbreeding coefficientexp_g
Inbreeding coefficientF
Ancestral inbreeding coefficientFa
Partial inbreeding coefficient (core function)Fij_core
Partial inbreeding coefficient (core function)Fij_core_i_cpp
Purged inbreeding coefficientg
Deviation from Hardy-Weinberg equilibriumhwd
Index ancestorsidx_ancestors
Inbreeding coefficientip_F
Ancestral inbreeding coefficientip_Fa
Partial inbreeding coefficientip_Fij
Purged inbreeding coefficientip_g
Opportunity of purgingip_op
Map ancestorsmap_ancestors
Realized effective population size (mean)Ne_delta se_Ne_delta
Opportunity of purgingop
Remove individuals not used for purging analysesped_clean
Input for igraphped_graph
Maternal effectsped_maternal
Rename individuals in a pedigree from 1 to Nped_rename
Sort individuals (with ancestors on top of descendants)ped_sort
Sorting stepsped_sort_i sort_step
Deviation from Hardy-Weinberg equilibriumpop_hwd
Population founders and ancestorspop_Na pop_Nae pop_Nancestors pop_Nf pop_Nfe pop_Ng
Effective population sizepop_Ne
Number of equivalent complete generationspop_t
purgeR: Estimation of inbreeding-purging genetic parameters in pedigreed populationspurgeR-package purgeR
Reproductive valuereproductive_value
Sample dam or sire inherited allelesample_allele
Search and individuals' ancestorssearch_ancestors
Grandoffspringw_grandoffspring
Offspringw_offspring
Reproductive valuew_reproductive_value