Ethnicity, e.g. subgroup within the allele frequency database.
nUnknowns
Number of unknown contributors for which to perform
calculation.
adj
Allele frequency adjustment parameter.
fst
Allele fraction adjustment F_{ST}.
databaseFile
Path to the allele database. If NULL, then defaults to
the NGMSelect database provided with likeLTD.
linkageFile
Path to recombination rate information. If NULL then defaults
to the linkage file provided with likeLTD. Only used
if relatedness=c(0.5,0.25) i.e. when Q and X are
siblings.
relationship
Specified relationship between Q and X. Can take values of 0=unrelated,
1=parent/offspring, 2=siblings, 3=uncle/nephew, 4=half-uncle/half-nephew, 5=cousins,
6=grandparent/grandchild, 7=half-siblings.
doDropin
Whether or not to model drop-in.
combineRare
Whether or not to combine rare unobserved alleles into a single
allele.
rareThreshold
If combineRare=TRUE, this is the probability threshold
below which an allele is classed as rare, and therefore
combined with other rare unobserved alleles.
kit
Parameter specifying which allele database supplied with likeLTD to use if
linkageFile is not specified. Possibilities are "DNA17", "Identifiler"
and "SGMplus".
...
Other parameters to determine how to perform calculations.
Details
It loads the CSP, known profiles, and allele database from file. It
removes the queried individual from the known profiles. It increments the
number of unknown contributors by one (to make up for the queried individual).
The reference individual is set to "X" (first unprofiled contributor) by
default.
Value
A list of named input parameters, or hypothesis, suitable for the
defence.