likeLTD::defence.hypothesis.peaks

Share:

Description

Helper function to create the input for the defence using peak height data.

Usage

1
2
3
4
5
6
7
defence.hypothesis.peaks(peaksFile, refFile, ethnic='NDU1', nUnknowns=0,
                        adj=1e0, fst=0.03, databaseFile=NULL, 
                        linkageFile=NULL,
                        detectionThresh=20, doDropin=FALSE, 
                        doDoubleStutter=TRUE,doOverStutter=TRUE,
                        combineRare=TRUE, rareThreshold=1,
                        kit=NULL, relationship=0, ...)

Arguments

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 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

 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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.