validatePed: Pedigree errors

In pedtools: Creating and Working with Pedigrees and Marker Data

Pedigree errors

Description

Validate the internal pedigree structure. The input may be either a (possibly malformed) ped() object, or its defining vectors id, fid, mid, sex.

Usage

validatePed(
  x = NULL,
  id = x$ID,
  fid = NULL,
  mid = NULL,
  sex = x$SEX,
  famid = x$FAMID,
  fidx = x$FIDX,
  midx = x$MIDX
)

Arguments

x	A ped object.
id	A character (or coercible to character) of individual ID labels.
fid, mid	Vectors of the same length as id, naming each individual's father and mother. Missing parents (of founders) may be entered as "0", "" or NA.
sex	A numeric of the same length as id, describing the genders of the individuals (in the same order as id.) Each entry must be either 1 (=male), 2 (=female) or 0 (=unknown).
famid	A character string. Default: An empty string.
fidx, midx	Integer vectors of parental indices (for internal use).

Value

If no errors are detected, the function returns NULL invisibly. Otherwise, messages describing the errors are printed to the screen and an error is raised.

Examples

x = nuclearPed()
validatePed(x)

# Various errors
# validatePed(id = c(1,2), fid = c(2,0), mid = c(0,1), sex = c(1,2))

pedtools documentation built on Nov. 5, 2026, 5:06 p.m.