sequoia (version 1.3.3)

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, Ped = NULL,
  LifeHistData = NULL, ParSib = "par", Complex = "full",
  Err = 1e-04, MaxMismatch = 3, 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.

Ped

dataframe with pedigree, 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. The error model aims to deal with scoring errors typical for SNP arrays.

MaxMismatch

maximum number of loci at which candidate parent and offspring are allowed to be opposite homozygotes. Setting a more liberal threshold can improve performance if the error rate is high, at the cost of decreased speed.

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 Ped.

quiet

suppress messages

Value

A list with

MaybeParent or MaybeRel

Non-assigned likely relatives

MaybeTrio

Non-assigned parent-parent-offspring trios

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)

# age differences limit which relationships are considered:
MaybePO3 <- GetMaybeRel(GenoM = SimGeno_example,
                      Ped = SeqOUT$PedigreePar)
# }