prune_fam | R Documentation |
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.
prune_fam(fam, ids, missing_vals = c("", 0))
fam |
The pedigree data.frame, in plink FAM format.
Only columns |
ids |
The list of individuals of interest, whose ancestors we want to keep.
All must be present in |
missing_vals |
The list of ID values treated as missing.
|
The filtered FAM table with non-ancestors of ids
excluded.
IDs that are NA
-equivalent (see missing_vals
) will be mapped to NA
.
# 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
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