PedToNum: Turn Character Pedigree into Numeric Pedigree

In sequoia: Pedigree Inference from SNPs

Turn Character Pedigree into Numeric Pedigree

Description

Genotyped individuals get rownumber in genotype matrix, non-genotyped individuals either all get an arbitrary negative number (DoDummies = 'new') or only individuals with a dummy ID get the corresponding negative number (DoDummies = 'old'). Note that the number series will overlap for dummy males and dummy females.

Usage

PedToNum(
  Pedigree = NULL,
  gID = NULL,
  DoDummies = "new",
  DumPrefix = c("F0", "M0")
)

Arguments

Pedigree	dataframe with id - dam - sire. It is assumed PedPolish has been called beforehand so that column names are correct and all columns are as.character.
gID	vector with IDs of SNP-genotyped individuals.
DoDummies	'new', 'old', or 'no' (ignore all non-genotyped individuals).
DumPrefix	Prefix to identify dummies when DoDummies = 'old'

Details

If DoDummies='new', GetDummifiable is used with minSibSize = "1sib", and any existing dummy coding is ignored (F0001, F0002 may become -3, -6). If DoDummies='old', the existing dummy coding is respected (F0001, F0002 will become -1, -2), but other non-genotyped individuals are ignored.

Value

a list with

PedPar	An nInd x 2 matrix with the numeric IDs of parents of genotyped individuals
DumPar	A matrix with parents of dummies, see FoldSibGPs
Renamed	a length-2 list (dams, sires) with each element a dataframe with columns: 'name' (original character ID), 'num' (number ID, negative) for each dummified individual
Nd	a length 2 vector, no. dummies found/created for dams and sires

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.