sequoia (version 2.0.7)

GetMaybeRel: 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,
  ParSib = "par",
  Complex = "full",
  Err = 1e-04,
  ErrFlavour = "version2.0",
  MaxMismatch = NA,
  Tassign = 0.5,
  MaxPairs = 7 * nrow(GenoM),
  DumPrefix = c("F0", "M0"),
  quiet = FALSE
)

Arguments

GenoM

matrix with genotype data, size nInd x nSnp

SeqList

list with output from sequoia. If provided, the elements `Specs', `AgePriors' and 'LifeHist' are used, and all other input parameters except 'GenoM', 'ParSib' and 'quiet' are ignored.

Pedigree

dataframe with id - dam - sire in columns 1-3

LifeHistData

dataframe with columns id - sex (1=female, 2=male, 3=unknown) - birth year

ParSib

either 'par' to check for putative parent-offspring pairs only, or 'sib' to check for all types of first and second degree relatives. When 'par', all pairs are returned that are more likely parent-offspring than unrelated, including pairs that are even more likely to be otherwise related.

Complex

either "full" (default), "simp" (simplified, no explicit consideration of inbred relationships), "mono" (monogamous) or "herm" (hermaphrodites, otherwise like "full").

Err

estimated genotyping error rate, as a single number or 3x3 matrix. If a matrix, this should be the probability of observed genotype (columns) conditional on actual genotype (rows). Each row must therefore sum to 1.

ErrFlavour

function that takes Err as input, and returns a 3x3 matrix of observed (columns) conditional on actual (rows) genotypes, or choose from inbuilt ones as used in sequoia 'version2.0', 'version1.3', or 'version1.1'. Ignored if Err is a matrix. See ErrToM.

MaxMismatch

DEPRECATED AND IGNORED. Now calculated using CalcMaxMismatch.

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.

MaxPairs

The maximum number of putative pairs to return.

DumPrefix

character vector of length 2 with prefixes for dummy dams (mothers) and sires (fathers) used in Pedigree.

quiet

suppress messages

Value

A list with

MaybeParent or MaybeRel

A dataframe with non-assigned likely relatives, with columns ID1 - ID2 - TopRel - LLR - OH - BirthYear1 - BirthYear2 - AgeDif - Sex1 - Sex2 - SNPdBoth

MaybeTrio

A dataframe with non-assigned parent-parent-offspring trios, with columns id - parent1 - parent2 - LLRparent1 - LLRparent2 - LLRpair - OHparent1 - OHparent2 - MEpair - SNPd.id.parent1 - SNPd.id.parent2

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 {
data(SimGeno_example, LH_HSg5, package="sequoia")
SeqOUT <- sequoia(GenoM = SimGeno_example,
                  LifeHistData = LH_HSg5, MaxSibIter = 0)
MaybePO <- GetMaybeRel(GenoM = SimGeno_example,
                      SeqList = SeqOUT)

Maybe <- GetMaybeRel(GenoM = SimGeno_example,
                      Pedigree = SeqOUT$PedigreePar, ParSib="sib")
# }
# NOT RUN {
# }