checkRimLim: Visually check retention index marker limits
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Details Value See Also Examples

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 `tsSample` object created by `ImportSamples`.
`rim`	A `tsRim` object describing the retention index markers. See `ImportFameSettings`.
`layout`	A vector of the form `c(nr, nc)` to arrange the panel by `nr` rows and `nc` columns. If missing then the layout is created automatically.
`show`	Logical. If `FALSE` the plot is not shown, but the data points can be used for further inspection or for custom plots.
`extend`	a numeric coefficient to extend the time window search of the respective time marker. Defaults to `0.5`.
`rect.col`	the color for the background rectangle which indicates the current retention time limits.
`mar`	the subplots margins, passed to `par()`.
`oma`	the outer plot margins, passed to `par()`.
`cex.main`	The magnification to be used for main titles, passed to `par()`.
`type`	A character vector indicating the type of plots. Default `"l"` for lines. Passed to `plot()`.
`...`	extra plotting arguments passed to `plot()` such as `col`, `lty`, `pch`, `lwd`.

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)

# to choose a specific samples and marker, use subsetting
ret <- checkRimLim(samples[3], rim[2])