read.peaks.profile: likeLTD::read.peaks.profile

Description

Reads the Crime Scene Profile from a CSV file of peak height data.

Usage

read.peaks.profile(FILE)

Arguments

FILE

Path to the crime scene profile with peak height data.

Value

A list of three elements, alleles, heights and sizes. Each element is itself a list with r elements, where r is the number of replicates in the CSP. Each of these elements is a matrix of n by x where n is the number of loci in the CSP, and x is the maximum number of peaks recorded at any locus for that replicate.

Details

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

Sample File	Marker	Allele 1	…	Allele x	Height 1	…	Height x	sample 1	locus 1	9.3
…	11	151	…	190	…	…	…	…	…	…
…	…	sample 1	locus n	23	…	NA	301	…	NA	sample r
locus 1	9.3	…	11	132	…	123	…	…	…	…
…	…	…	…	sample r	locus n	23	…	NA	256	…
NA	Sample File	Marker	Allele 1	…	Allele x	Height 1	…	Height x	sample 1	locus 1

Columns are separted by commas (not present in the table above). The first line, containing the names of the columns needs to be present. x, r and n can be any number. Columns headed by "Allele 1 … x" should contain the allelic designation of the peak. Columns headed by "Height 1 … x" should contain the peak height in RFU.

Examples

Run this code

# 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
             )

# read csp
csp = read.peaks.profile(admin$peaksFile)
# }