load.allele.database: likeLTD::load.allele.database

Description

Reads allele database from file, or loads database provided with likeLTD.

Usage

load.allele.database(path=NULL, kit=NULL)

Arguments

path

Path to the database file, or NULL. If NULL, then returns the allele database packaged with likeLTD.

kit

Only used if path=NULL. Specifies one of the allele database supplied with likeLTD to use. Possibilities are "DNA17", "Identifiler", "SGMplus", "NISTidentifiler" and "NISTglobalfiler". Defaults to "DNA17" if both path=NULL and kit=NULL.

Value

A table, as read from the file.

Details

If not NULL, then the input should consist of a file in the following format:

Marker	Allele	LUS	BP	EA1	EA2	…
TH01	5	5	166	1	2	TH01
6	6	170	212	44	TH01	8
8	178	90	69	TH01	8.3	5
181	0	0	TH01	10	10	186
7	6	TH01	R/-100	NA	NA	0
0	vWA	13	7.3	163	0	5
vWA	14	7.5	167	86	24	…

The first line needs to be present. The first column indicated the locus, the second the name of the allele, the third the longest uninterrupted sequence of the allele, the fourth the fragment length. The next columns are the frequencies for specific ethnic groups. There are no limits to the number of ethnic groups included. If the name of an allele is R for the discrete model, or -100 for the peak heights model, then it is ignored. If running the discrete model, LUS values are not used, so may be provided as NA.

Examples

Run this code

# NOT RUN {
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"hammer")

# File paths and case name for allele report
admin = pack.admin.input(
            cspFile = file.path(datapath, 'hammer-CSP.csv'),
            refFile = file.path(datapath, 'hammer-reference.csv'),
            caseName = "hammer",
	    kit= "SGMplus"
             )

# get allele database
load.allele.database(kit=admin$kit)
# }