Description Usage Arguments Details Value See Also Examples
View source: R/reports-peaks.R
Plot one replicate from a peak heights CSP.
1 2 3 4 5 |
csp |
CSP as returned from |
refs |
Reference profiles as returned by |
dbFile |
Path to allele database file. If |
kit |
Choice of an allele database that is included wiht likeLTD. If both
|
outputFile |
Path to output file. If |
toPlot |
An integer vector specifying which loci to plot. If |
detectThresh |
Detection threshold used for electrophoresis analysis. If |
uncThresh |
Threshold for suggesting that a peak is uncertain. |
stutterThresh |
Threshold for suggesting a peak is allelic. |
doStutter |
Logical. Specifies whether to suggest peaks as non-allelic/uncertain/allelic. |
replicate |
Which replicate to plot. |
... |
Extra parameters to pass to |
If refFile
is specified, the plotted peaks are coloured according to which
reference individuals possess that allele. If detectThresh
is specified, a
horizontal line is plotted indicating the threshold. If doStutter=TRUE
, the
labels for each peak are coloured by a crude estimation of which peaks are allelic,
uncertain, or non-allelic.
Pdf file or plot window.
allele.report.peaks
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ## 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
)
# plot CSP heights
CSP.heights.plot(csp=read.peaks.profile(admin$peaksFile),
ref=read.known.profiles(admin$refFile))
# to plot just the first four loci
CSP.heights.plot(csp=read.peaks.profile(admin$peaksFile),
ref=read.known.profiles(admin$refFile),
toplot=1:4)
# to estimate which peaks are non-allelic
CSP.heights.plot(csp=read.peaks.profile(admin$peaksFile),
ref=read.known.profiles(admin$refFile),
doStutter=TRUE)
# to display detection threshold
CSP.heights.plot(csp=read.peaks.profile(admin$peaksFile),
ref=read.known.profiles(admin$refFile),
detectThresh=20)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.