read.known.profiles: likeLTD::read.known.profiles

Description

Reads the known profiles from file.

Usage

read.known.profiles(path)

Arguments

path

Path to a CSV file with known profiles.

Value

A matrix where columns are loci and rows are individual profiles. Each element is a vector of two characters, and each character is the name of an allele represented in the individual. There should be two characters for each entry.

Additionnaly, the first column (named "queried") indicates whether that individiual is to be queried (TRUE) or is known to be in the CSP (FALSE).

Details

The input is a file in the CSV format (comma-separated values). It should have the following form:

Individual	known/queried		Locus	Locus	…	name
queried	"13,15"	"16,16"	…	name	known
"18, 19"	"16, 17.2"	…	Individual	known/queried		Locus

Columns are separted by commas (not present in the table above). The first line, containing the name of the columns need be present. Each row is the profile of a different individual. Names or identifiers for the individuals are contained in the first column. The second column should contain the word "queried" if the individual should be queried. The other columns are for the differnt loci. "Locus" should be replaced with the name of the locus in the first column. Each item consists of two comma separated values within qutoation marks. The values are the name of the allles in that individual's profile for that locus.

Examples

Run this code

# NOT RUN {
######################
# Peak heights model #
######################
# 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
             )

# get reference profiles
read.known.profiles(admin$refFile)

##################
# Discrete model #
##################
# 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 reference profiles
read.known.profiles(admin$refFile)
# }