R: Find Putative Relatives

GetMaybeRel {sequoia}

R Documentation

Find Putative Relatives

Description

Identify pairs of individuals likely to be related, but not assigned as such in the provided pedigree.

Usage

GetMaybeRel(
  GenoM = NULL,
  SeqList = NULL,
  Pedigree = NULL,
  LifeHistData = NULL,
  AgePrior = NULL,
  Module = "par",
  Complex = "full",
  Herm = "no",
  Err = 1e-04,
  ErrFlavour = "version2.9",
  Tassign = 0.5,
  Tfilter = -2,
  MaxPairs = 7 * nrow(GenoM),
  quiet = FALSE,
  ParSib = NULL,
  MaxMismatch = NA
)

Arguments

`GenoM`	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`.
`SeqList`	list with output from `sequoia`. `SeqList$Pedigree` is used if present, and `SeqList$PedigreePar` otherwise, and overrides the input parameter `Pedigree`. If 'Specs' is present, its elements override all input parameters with the same name. The list elements ‘LifeHist’, ‘AgePriors’, and ‘ErrM’ are also used if present, and similarly override the corresponding input parameters.
`Pedigree`	dataframe with id - dam - sire in columns 1-3. May include non-genotyped individuals, which will be treated as dummy individuals. When provided, all likelihoods (and thus all maybe-relatives) are conditional on this pedigree. Note: `SeqList$Pedigree` or `SeqList$PedigreePar` take precedent (for this function only).
`LifeHistData`	data.frame with up to 6 columns: ID max. 30 characters long Sex 1 = female, 2 = male, 3 = unknown, 4 = hermaphrodite, other numbers or NA = unknown BirthYear birth or hatching year, integer, with missing values as NA or any negative number. BY.min minimum birth year, only used if BirthYear is missing BY.max maximum birth year, only used if BirthYear is missing Year.last 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.
`AgePrior`	Agepriors matrix, as generated by `MakeAgePrior` and included in the `sequoia` output. Affects which relationships are considered possible (only those where `P(A\|R) / P(A) > 0`).
`Module`	type of relatives to check for. One of par parent - offspring pairs ped all first and second degree relatives When 'par', all pairs are returned that are more likely parent-offspring than unrelated, potentially including pairs that are even more likely to be otherwise related.
`Complex`	Breeding system complexity. Either "full" (default), "simp" (simplified, no explicit consideration of inbred relationships), "mono" (monogamous).
`Herm`	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.
`Err`	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.
`ErrFlavour`	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.
`Tassign`	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.
`Tfilter`	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.
`MaxPairs`	the maximum number of putative pairs to return.
`quiet`	logical, suppress messages.
`ParSib`	DEPRECATED, use `Module` either 'par' to check for putative parent-offspring pairs only, or 'sib' to check for all types of first and second degree relatives.
`MaxMismatch`	DEPRECATED AND IGNORED. Now calculated automatically using `CalcMaxMismatch`.

Details

When Module="par", the age difference of the putative pair is temporarily set to NA so that genetic parent-offspring pairs declared to be born in the same year may be discovered. When Module="ped", only relationships possible given the age difference, if known from the LifeHistData, are considered.

Value

A list with

MaybePar

A dataframe with non-assigned likely parent-offspring pairs, with columns:

ID1
ID2
TopRel: the most likely relationship, using abbreviations listed below
LLR: Log10-Likelihood Ratio between most likely and next most likely relationship
OH: Number of loci at which the two individuals are opposite homozygotes
BirthYear1: Birth year of ID1 (copied from LifeHistData)
BirthYear2
AgeDif: Age difference; BirthYear1 - BirthYear2
Sex1: Sex of ID1 (copied from LifeHistData)
Sex2
SnpdBoth: Number of loci at which the two individuals are both successfully genotyped

MaybeRel

A dataframe with non-assigned likely pairs of relatives, with columns identical to MaybePar

MaybeTrio

A dataframe with non-assigned parent-parent-offspring trios, with columns:

ID
parent1
parent2
TopRel: the most likely relationship, using abbreviations listed below
LLRparent1: Log10-Likelihood Ratio between parent1 being a parent of ID vs the next most likely relationship between the pair, ignoring parent2
LLRparent2: as LLRparent1
LLRpair: LLR for the parental pair, versus the next most likely configuration between the three individuals (with one or neither parent assigned)
OHparent1: Number of loci at which ID and parent1 are opposite homozygotes
OHparent2: as OHparent1
MEpair: 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.
SNPd.id.parent1: Number of loci at which ID and parent1 are both successfully genotyped
SNPd.id.parent2: as SNPd.id.parent1

The following categories are used in column 'TopRel', indicating the most likely relationship category:

`PO`	Parent-Offspring
`FS`	Full Siblings
`HS`	Half Siblings
`GP`	GrandParent - grand-offspring
`FA`	Full Avuncular (aunt/uncle)
`2nd`	2nd degree relatives, not enough information to distinguish between HS,GP and FA
`Q`	Unclear, but probably 1st, 2nd or 3rd degree relatives

Examples

## Not run: 
# without conditioning on pedigree
MaybeRel_griffin <- GetMaybeRel(GenoM=Geno_griffin, Err=0.001, Module='par')

## End(Not run)
names(MaybeRel_griffin)

# conditioning on pedigree
MaybePO <- GetMaybeRel(GenoM = Geno_griffin, SeqList = SeqOUT_griffin,
                      Module = 'par')
head(MaybePO$MaybePar)

# instead of providing the entire SeqList, one may specify the relevant
# elements separately
Maybe <- GetMaybeRel(GenoM = Geno_griffin,
                     Pedigree = SeqOUT_griffin$PedigreePar,
                     LifeHistData = LH_griffin,
                     Err=0.0001, Complex = "full",
                     Module = "ped")
head(Maybe$MaybeRel)

# visualise results, turn dataframe into matrix first:
MaybeM <- GetRelM(Pairs = Maybe$MaybeRel)
PlotRelPairs(MaybeM)
# or combine with pedigree (note suffix '?')
RelM <- GetRelM(Pedigree =SeqOUT_griffin$PedigreePar, Pairs = Maybe$MaybeRel)
PlotRelPairs(RelM)

[Package sequoia version 2.11.2 Index]