Description Usage Arguments Details Value See Also Examples
View source: R/hypothesis-peaks.R
Helper function to create the input for the prosecution using peak height data.
1 2 3 4 5 6 7 |
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.
A list of named input parameters, or hypothesis, suitable for the prosecution.
defence.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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.