prune_fam {simfam}

Remove non-ancestors of a set of individuals from pedigree

Description

This function accepts an input pedigree and a list of individuals of interest, and returns the subset of the pedigree including only the individuals of interest and their direct ancestors. This is useful in simulations, to avoid modeling/drawing genotypes of individuals without descendants in the last generation.

Usage

prune_fam(fam, ids, missing_vals = c("", 0))

Arguments

fam

The pedigree data.frame, in plink FAM format. Only columns id, pat, and mat are required. id must be unique and non-missing. Founders must be present, and their pat and mat values must be missing (see below). Non-founders must have both their parents be non-missing. Parents must appear earlier than their children in the table.

ids

The list of individuals of interest, whose ancestors we want to keep. All must be present in fam$id.

missing_vals

The list of ID values treated as missing. NA is always treated as missing. By default, the empty string (”) and zero (0) are also treated as missing (remove values from here if this is a problem).

Value

The filtered FAM table with non-ancestors of ids excluded. IDs that are NA-equivalent (see missing_vals) will be mapped to NA.

Examples

# construct a family with three founders, but one "bob" has no descendants
library(tibble)
fam <- tibble(
    id  = c('mom', 'dad', 'bob', 'child'),
    pat = c(   NA,    NA,    NA,   'dad'),
    mat = c(   NA,    NA,    NA,   'mom')
)
# only want 'child' and its ancestors
ids <- 'child'
fam2 <- prune_fam( fam, ids )
# the filtered pedigree has "bob" removed:
fam2