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. Must include
longest uninterrupted sequence (LUS) values for alleles.
linkageFile
Path to recombination rate information. If NULL then defaults
to the linkage file provided with likeLTD. Only used
if relationship is not 0 or 1 i.e. when Q and X are
closely related but not parent/offspring.
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.
detectionThresh
Detection threshold for peaks. Can be a single value, or a named list
containing one value per locus.
doDropin
Whether or not to model drop-in. Note dropin is not currently possible
with the peak heights model.
doDoubleStutter
Logical. Whether or not to model double stutter.
doOverStutter
Logical. Whether or not to model over stutter.
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-lus".
...
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).
Value
A list of named input parameters, or hypothesis, suitable for the
defence.
See Also
prosecution.hypothesis.peaks
Examples
## Not run:
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"laboratory")
# File paths and case name for allele report
admin = pack.admin.input.peaks(
peaksFile = file.path(datapath, 'laboratory-CSP.csv'),
refFile = file.path(datapath, 'laboratory-reference.csv'),
caseName = "Laboratory",
detectionThresh = 20
)
# Enter arguments
args = list(
nUnknowns = 1
)
# Create hypotheses
hypP = do.call(prosecution.hypothesis.peaks, append(admin,args))
hypD = do.call(defence.hypothesis.peaks, append(admin,args))
## End(Not run)