Description Usage Arguments Details Value See Also Examples
View source: R/hypothesis-peaks.R
Helper function to create the input for the defence using peak height data.
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peaksFile |
Path to the crime scene profile. |
refFile |
Path to the known profiles. |
ethnic |
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 |
linkageFile |
Path to recombination rate information. If NULL then defaults
to the linkage file provided with |
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 |
kit |
Parameter specifying which allele database supplied with likeLTD to use if
|
... |
Other parameters to determine how to perform calculations. |
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).
A list of named input parameters, or hypothesis, suitable for the defence.
prosecution.hypothesis.peaks
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ## 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)
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