checkRimLim {TargetSearch} | R Documentation |
A function to visually check if the retention time limites of the retention index markers (aka FAMEs) is correct.
checkRimLim(samples, rim, layout, show = TRUE, extend = 0.5, rect.col = "#e7e7e7", mar = c(2, 2, 2, 2), oma = c(3, 3, 2, 0.5), cex.main = 1, type = "l", ...)
samples |
A |
rim |
A |
layout |
A vector of the form |
show |
Logical. If |
extend |
a numeric coefficient to extend the time window search of the
respective time marker. Defaults to |
rect.col |
the color for the background rectangle which indicates the current retention time limits. |
mar |
the subplots margins, passed to |
oma |
the outer plot margins, passed to |
cex.main |
The magnification to be used for main titles, passed to
|
type |
A character vector indicating the type of plots. Default |
... |
extra plotting arguments passed to |
The function takes a random CDF file from your tsSample
object and creates a panel plot of the m/z traces around the area in which a
marker is expected to be. Repeated calls to this function can be used to check
other samples. It is also possible to check a specific sample by indexing
the tsSample
object.
A list of n
times 2
matrices or invisible. Each element correspond to a
marker. Columns are retention time and intensities of the respective marker's m/z.
The rows can be as many data points are within the search window.
tsSample
, tsRim
, ImportFameSettings
require(TargetSearchData) # get the cdf path TargetSearchData cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data") # import samples (see ImportSamples() for details) samples <- ImportSamples(file.path(cdfpath, "samples.txt"), CDFpath = cdfpath) # Import RI markers (see ImportFameSettings()) rim <- ImportFameSettings(file.path(cdfpath, "rimLimits.txt")) # choose a sample at random and plot the m/z traces around the retention # time window ret <- checkRimLim(samples, rim)