pedcheck: Summary statistics for pedigree

In GHap: Genome-Wide Haplotyping

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 <[e-mail]>

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)

GHap documentation built on July 2, 2022, 1:07 a.m.