PedToNum | R Documentation |
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.
PedToNum(
Pedigree = NULL,
gID = NULL,
DoDummies = "new",
DumPrefix = c("F0", "M0")
)
Pedigree |
dataframe with id - dam - sire. It is assumed
|
gID |
vector with IDs of SNP-genotyped individuals. |
DoDummies |
'new', 'old', or 'no' (ignore all non-genotyped individuals). |
DumPrefix |
Prefix to identify dummies when |
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.
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
|
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 |
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