GetMaybeRel {sequoia} | R Documentation |
Identify pairs of individuals likely to be related, but not assigned as such in the provided pedigree.
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)
GenoM |
matrix with genotype data, size nInd x nSnp |
SeqList |
list with output from |
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 |
quiet |
suppress messages |
A list with
MaybeParent or MaybeRel |
Non-assigned likely relatives |
MaybeTrio |
Non-assigned parent-parent-offspring trios |
## 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) ## End(Not run)