| ghap.pedcheck {GHap} | R Documentation |
Summary statistics for pedigree
Description
This function summarizes pedigree data and calculates inbreeding coefficients and equivalent complete generations.
Usage
ghap.pedcheck(ped, depth.n.f = FALSE)
Arguments
ped |
A dataframe with columns "id", "sire" and "dam" containing pedigree data. |
depth.n.f |
A logical indicating if equivalent complete generations (depth) and inbreeding coefficients (f) should be calculated. |
Value
A list containing two data frames: stats, which includes the pedigree summary; and ped, consisting of the original pedigree. If depth.n.f = TRUE, three columns are added to the ped data frame: gen (generation number), f (inbreding coefficient) and ecg (equivalent complete generations). The generation number and the inbreeding coefficient are computed with the help of the pedigreemm package.
Author(s)
Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
References
A. I. Vazquez. Technical note: An R package for fitting generalized linear mixed models in animal breeding. J. Anim. Sci. 2010. 88, 497-504.
Examples
# #### DO NOT RUN IF NOT NECESSARY ###
#
# # Copy metadata in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
# format = "meta",
# verbose = TRUE)
# file.copy(from = exfiles, to = "./")
#
# # Load pedigree data
# ped <- read.table(file = "example.pedigree", header=T)
#
# ### RUN ###
#
# # Descriptive statistics for the pedigree
# pedstat <- ghap.pedcheck(ped[,-1])
# print(pedstat$stats)
#
# # Retrieve inbreeding and pedigree depth
# pedstat <- ghap.pedcheck(ped[,-1], depth.n.f = TRUE)
# print(pedstat$ped)
# hist(pedstat$ped$f)
# hist(pedstat$ped$ecg)