SeqPrep {sequoia} | R Documentation |
Check parameter values and save as named vector.
SeqPrep(GenoM = NULL, LifeHistData = NULL, nAgeClasses = 1, MaxSibIter = 5, Err = 1e-04, MaxMismatch = 3, Tfilter = -2, Tassign = 0.5, MaxSibshipSize = 100, DummyPrefix = c("F", "M"), Complexity = "full", UseAge = "yes", FindMaybeRel = TRUE, CalcLLR = TRUE)
GenoM |
matrix with genotype data, size nInd x nSnp |
LifeHistData |
Dataframe with 3 columns:
|
nAgeClasses |
Number of age classes (= no. rows in AgePriors) |
MaxSibIter |
Maximum number of iterations of sibship clustering (up to 42). |
Err |
Estimated genotyping error rate. |
MaxMismatch |
Maximum number of loci at which candidate parent and offspring are allowed to be opposite homozygotes, or be excluded. |
Tfilter |
Threshold log-likelihood ratio 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. |
Tassign |
Minimum log-likelihood ratio required for acceptance of proposed relationship, relative to next most likely relationship. Higher values result in more conservative assignments. |
MaxSibshipSize |
Maximum number of offspring for a single individual (a generous safety margin is advised). |
DummyPrefix |
character vector of length 2 with prefixes for dummy dams (mothers) and sires (fathers); maximum 20 characters each. |
Complexity |
Either "full" (default), "simp" (no explicit consideration of inbred relationships), "mono" (monogamous breeding system), or "herm" (hermaphrodites) |
FindMaybeRel |
Identify pairs of non-assigned likely relatives after pedigree reconstruction. Can be time-consuming in large datasets. |
CalcLLR |
Calculate log-likelihood ratios for all assignments. Can be time-consuming in large datasets. |
Please do not increasing the number of SNPs or individuals beyond the numbers present in the datasets, as this may cause R to crash.
A 1-row dataframe with parameter values