purgeR | R Documentation |
The purgeR package includes functions for the computation of parameters related to inbreeding and genetic purging in pedigreed populations, including standard, ancestral and purged inbreeding coefficients, among other measures of inbreeding and purging. In addition, functions to compute the effective population size and other parameters relevant to population genetics and structure are included.
A complete user's guide with examples is provided as vignettes, introducing functions in this package and providing examples of use. Navigate these vignettes from R with:
browseVignettes("purgeR")
There are currently two vignettes available:
purgeR-tutorial: A complete overview of all functions in the package, including easy to follow examples.
ip: A more advanced guide showing examples of inbreeding purging analyses.
Preprocessing
ped_rename
: Rename individuals in a pedigree from 1 to N
ped_sort
: Sort individuals (with ancestors on top of descendants)
ped_clean
: Remove individuals not used for purging analyses
ped_maternal
: Maternal effects
ped_graph
: Input for igraph
Inbreeding and purging
ip_F
: Inbreeding coefficient
ip_Fa
: Ancestral inbreeding coefficient
ip_Fij
: Partial inbreeding coefficient
ip_g
: Purged inbreeding coefficient
ip_op
: Opportunity of purging
exp_F
: Expected inbreeding coefficient
exp_Fa
: Expected ancestral inbreeding coefficient
exp_g
: Expected purged inbreeding coefficient
Population parameters
pop_hwd
: Deviation from Hardy-Weinberg equilibrium
pop_t
: Number of equivalent complete generations
pop_Ne
: Effective population size
pop_Nancestors
: Population founders and ancestors
pop_Na
: Total number of ancestors
pop_Nae
: Effective number of ancestors
pop_Nf
: Total number of founders
pop_Nfe
: Effective number of founders
pop_Ng
: Number of founder genome equivalents
Fitness
w_grandoffspring
: Grandoffspring
w_offspring
: Offspring
w_reproductive_value
: Reproductive value
Eugenio López-Cortegano <elcortegano@gmail.com> (ORCID)
López-Cortegano E. 2022. purgeR: Inbreeding and purging in pedigreed populations. Bioinformatics, https://doi.org/10.1093/bioinformatics/btab599.
Source code is available via the GitLab repository at https://gitlab.com/elcortegano/purgeR/. Users are encouraged to report bugs, request features, and contribute code to this project.
Some users might find useful the C++ software PURGd, which computes inbreeding-purging parameters and follow-up statistical analyses: https://gitlab.com/elcortegano/PURGd/.
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