Description Usage Arguments Details Value See Also Examples
View source: R/hypothesis-peaks.R
Reads the Crime Scene Profile from a CSV file of peak height data.
1 | read.peaks.profile(FILE)
|
FILE |
Path to the crime scene profile with peak height data. |
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.
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.
read.known.profiles
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
Loading required package: DEoptim
Loading required package: parallel
DEoptim package
Differential Evolution algorithm in R
Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
Loading required package: ggplot2
Loading required package: gtools
Loading required package: rtf
Warning message:
no DISPLAY variable so Tk is not available
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