View source: R/getAssignable.R
getAssignCat | R Documentation |
Identify which individuals are SNP genotyped (G), and which can potentially be substituted by a dummy individual ('dummifiable', D).
getAssignCat(Pedigree, SNPd, minSibSize = "1sib1GP")
Pedigree |
dataframe with columns id-dam-sire. Reference pedigree. |
SNPd |
character vector with ids of genotyped individuals. |
minSibSize |
minimum requirements to be considered dummifiable is 1 genotyped offspring, and
. |
Non-genotyped individuals can potentially be substituted by a dummy
during pedigree reconstruction by sequoia
when they have at least one genotyped
offspring, and either one additional offspring (genotyped or dummy) or an
genotyped/dummy parent (i.e. a grandparent to the genotyped offspring).
Note that this is the bare minimum requirement; e.g. grandparents are often
indistinguishable from full avuncular (see sequoia
and
vignette for details). G-G parent-offspring pairs are only assignable if
there is age information, or information from the surrounding pedigree, to
tell which of the two is the parent.
It is assumed that all individuals in SNPd
have been
genotyped for a sufficient number of SNPs. To identify samples with a
too-low call rate, use CheckGeno
. To calculate the call rate
for all samples, see the examples below.
The Pedigree
dataframe with 3 additional columns,
id.cat
, dam.cat
and sire.cat
, with coding similar to
that used by PedCompare
:
G |
Genotyped |
D |
Dummy or 'dummifiable' |
X |
Not genotyped and not dummifiable |
PedA <- getAssignCat(Ped_HSg5, rownames(SimGeno_example))
tail(PedA)
table(PedA$dam.cat, PedA$sire.cat, useNA="ifany")
# calculate call rate
## Not run:
CallRates <- apply(MyGenotypes, MARGIN=1,
FUN = function(x) sum(x!=-9)) / ncol(MyGenotypes)
hist(CallRates, breaks=50, col="grey")
GoodSamples <- rownames(MyGenotypes)[ CallRates > 0.8]
# threshold depends on total number of SNPs, genotyping errors, proportion
# of candidate parents that are SNPd (sibship clustering is more prone to
# false positives).
PedA <- getAssignCat(MyOldPedigree, rownames(GoodSamples))
## End(Not run)
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