checkRimLim {TargetSearch} | R Documentation

## Visually check retention index marker limits

### Description

A function to visually check if the retention time limites of the retention index markers (aka FAMEs) is correct.

### Usage

    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",
      ...
    )

### Arguments

`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`.

### Details

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.

### Value

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.

### See Also

`tsSample`, `tsRim`, `ImportFameSettings`

### Examples

    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])

[Package TargetSearch version 1.43.3 Index]