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

Description Usage Arguments Details Value See Also Examples

View source: R/hypothesis-peaks.R

Description

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

Usage

1

Arguments

FILE

Path to the crime scene profile with peak height data.

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

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.

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.

See Also

read.known.profiles

Examples

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## 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)

## End(Not run)

likeLTD documentation built on Feb. 11, 2018, 3:10 p.m.