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.
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
## 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)