Count opposite homozygous (OH) loci between parent-offspring pairs and Mendelian errors (ME) between parent-parent-offspring trios, and calculate the parental log-likelihood ratios (LLR).
CalcOHLLR(
Pedigree = NULL,
GenoM = NULL,
CalcLLR = TRUE,
LifeHistData = NULL,
AgePrior = FALSE,
SeqList = NULL,
Err = 1e-04,
ErrFlavour = "version2.9",
Tassign = 0.5,
Tfilter = -2,
Complex = "full",
Herm = "no",
quiet = FALSE
)The Pedigree dataframe with additional columns:
Log10-Likelihood Ratio (LLR) of this female being the mother, versus the next most likely relationship between the focal individual and this female (see Details for relationships considered)
idem, for male parent
LLR for the parental pair, versus the next most likely configuration between the three individuals (with one or neither parent assigned)
Number of loci at which the offspring and mother are opposite homozygotes
idem, for father
Number of Mendelian errors between the offspring and the parent pair, includes OH as well as e.g. parents being opposing homozygotes, but the offspring not being a heterozygote. The offspring being OH with both parents is counted as 2 errors.
Number of SNPs scored (non-missing) for the focal individual
Number of SNPs scored (non-missing) for both individual and dam
Number of SNPs scored for both individual and sire
Sex in LifeHistData, or inferred Sex when assigned as part of parent-pair
mode of birth year probability distribution
lower limit of 95% highest density region of birth year probability distribution
higher limit
The columns 'LLRdam', 'LLRsire' and 'LLRpair' are only included when
CalcLLR=TRUE. When a parent or parent-pair is incompatible with the
lifehistory data or presumed genotyping error rate, the error value '777' may
be given.
The columns 'Sexx', 'BY.est', 'BY.lo' and 'BY.hi' are only included when
LifeHistData is provided, and at least one genotyped individual has an
unknown birth year or unknown sex.
dataframe with columns id-dam-sire. May include
non-genotyped individuals, which will be treated as dummy individuals. If
provided, any pedigree in SeqList is ignored.
numeric matrix with genotype data: One row per individual,
one column per SNP, coded as 0, 1, 2, missing values as a negative number
or NA. You can reformat data with GenoConvert, or use other
packages to get it into a genlight object and then use as.matrix.
calculate log-likelihood ratios for all assigned parents
(genotyped + dummy/non-genotyped; parent vs. otherwise related). If
FALSE, only number of mismatching SNPs are counted (OH &
ME), and parameters LifeHistData, AgePrior, Err,
Tassign, and Complex are ignored. Note also that
calculating likelihood ratios is much more time consuming than counting OH
& ME.
data.frame with up to 6 columns:
max. 30 characters long
1 = female, 2 = male, 3 = unknown, 4 = hermaphrodite, other numbers or NA = unknown
birth or hatching year, integer, with missing values as NA or any negative number.
minimum birth year, only used if BirthYear is missing
maximum birth year, only used if BirthYear is missing
Last year in which individual could have had offspring. Can e.g. in mammals be the year before death for females, and year after death for males.
"Birth year" may be in any arbitrary discrete time unit relevant to the species (day, month, decade), as long as parents are never born in the same time unit as their offspring, and only integers are used. Individuals do not need to be in the same order as in `GenoM', nor do all genotyped individuals need to be included.
logical (TRUE/FALSE) whether to estimate the ageprior
from Pedigree and LifeHistData, or a matrix as generated by
MakeAgePrior and included in the sequoia
output. The AgePrior affects which relationships are considered
possible: only those where \(P(A|R) / P(A) > 0\). When TRUE,
MakeAgePrior is called using its default values. When
FALSE, all relationships are considered possible for all age
differences, except that parent-offspring pairs cannot have age difference
zero, and grand-parental pairs have an age difference of at least two.
list with output from sequoia. If input
parameter Pedigree=NULL, SeqList$Pedigree will be used if
present, and SeqList$PedigreePar otherwise. If SeqList$Specs
is present, input parameters with the same name as its items are ignored,
except 'CalcLLR' and 'AgePriors=FALSE'. The list elements `LifeHist',
`AgePriors', and `ErrM' are also used if present, and override the
corresponding input parameters.
estimated genotyping error rate, as a single number, or a length 3
vector with P(hom|hom), P(het|hom), P(hom|het), or a 3x3 matrix. See
details below. The error rate is presumed constant across SNPs, and
missingness is presumed random with respect to actual genotype. Using
Err >5% is not recommended, and Err >10% strongly
discouraged.
function that takes Err (single number) as input,
and returns a length 3 vector or 3x3 matrix, or choose from inbuilt options
'version2.9', 'version2.0', 'version1.3', or 'version1.1', referring to the
sequoia version in which they were the default. Ignored if Err is a
vector or matrix. See ErrToM for details.
minimum LLR required for acceptance of proposed relationship, relative to next most likely relationship. Higher values result in more conservative assignments. Must be zero or positive.
threshold log10-likelihood ratio (LLR) between a proposed relationship versus unrelated, to select candidate relatives. Typically a negative value, related to the fact that unconditional likelihoods are calculated during the filtering steps. More negative values may decrease non-assignment, but will increase computational time.
Breeding system complexity. Either "full" (default), "simp" (simplified, no explicit consideration of inbred relationships), "mono" (monogamous).
Hermaphrodites, either "no", "A" (distinguish between dam and sire role, default if at least 1 individual with sex=4), or "B" (no distinction between dam and sire role). Both of the latter deal with selfing.
logical, suppress messages
Any individual in Pedigree that does not occur in
GenoM is substituted by a dummy individual; these can be recognised
by the value 0' in columns 'SNPd.id.dam' and `SNPd.id.sire` in the output.
For non-genotyped individuals the parental log-likelihood ratio can be
calculated if they have at least one genotyped offspring (see also
getAssignCat).
The birth years in LifeHistData and the AgePrior are not used
in the calculation and do not affect the value of the likelihoods for the
various relationships, but they _are_ used during some filtering steps, and
may therefore affect the likelihood _ratio_. The default
(AgePrior=FALSE) assumes all age-relationship combinations are
possible, which may mean that some additional alternatives are considered
compared to the sequoia default, resulting in somewhat lower
LLR values.
A negative LLR for A's parent B indicates either that B is not truely the parent of A, or that B's parents are incorrect. The latter may cause B's presumed true, unobserved genotype to divert from its observed genotype, with downstream consequences for its offspring. In rare cases it may also be due to 'weird', non-implemented double or triple relationships between A and B.
SummarySeq for visualisation of OH & LLR
distributions; CalcPairLL for the likelihoods underlying the
LLR, GenoConvert to read in various genotype data formats,
CheckGeno; PedPolish to check and 'polish' the
pedigree; getAssignCat to find which id-parent pairs are both
genotyped or can be substituted by dummy individuals; sequoia
for pedigree reconstruction.
# count Mendelian errors in an existing pedigree
Ped.OH <- CalcOHLLR(Pedigree = Ped_HSg5, GenoM = SimGeno_example,
CalcLLR = FALSE)
Ped.OH[50:55,]
# view histograms
SummarySeq(Ped.OH, Panels="OH")
# Parent likelihood ratios in an existing pedigree, including for
# non-genotyped parents
Ped.LLR <- CalcOHLLR(Pedigree = Ped_HSg5, GenoM = SimGeno_example,
CalcLLR = TRUE, LifeHistData=LH_HSg5, AgePrior=TRUE)
SummarySeq(Ped.LLR, Panels="LLR")
if (FALSE) {
# likelihood ratios change with presumed genotyping error rate:
Ped.LLR.B <- CalcOHLLR(Pedigree = Ped_HSg5, GenoM = SimGeno_example,
CalcLLR = TRUE, LifeHistData=LH_HSg5, AgePrior=TRUE,
Err = 0.005)
SummarySeq(Ped.LLR.B, Panels="LLR")
# run sequoia with CalcLLR=FALSE, and add OH + LLR later:
SeqOUT <- sequoia(Geno_griffin, LH_griffin, CalcLLR=FALSE,quiet=TRUE,Plot=FALSE)
PedA <- CalcOHLLR(Pedigree = SeqOUT[["Pedigree"]][, 1:3], GenoM = Genotypes,
LifeHistData = LH_griffin, AgePrior = TRUE, Complex = "full")
SummarySeq(PedA, Panels=c("LLR", "OH"))
}
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