tsRim-class {TargetSearch} | R Documentation

## Class for representing retention index markers

### Description

This is a class to represent retention index markers.

### Objects from the Class

Objects can be created by the function `ImportFameSettings` or by calls of the form `new("tsRim", limits = [two column matrix with time limits], standard = [a vector with RI standards], mass = [m/z marker])`.

### Slots

`limits`:

  `"matrix"`, two column matrix with lower and upper limits where the standards will be search. One row per standard.

`standard`:

  `"numeric"`, the marker RI values.

`mass`:

  `"numeric"`, the m/z marker.

### Methods

`[`

  `signature(x = "tsRim")`: Selects a subset of markers.

`rimLimits`

  `signature(obj = "tsRim")`: gets the time limits.

`rimLimits<-`

  `signature(obj = "tsRim")`: sets the time limits.

`rimMass`

  `signature(obj = "tsRim")`: gets the m/z marker.

`rimMass<-`

  `signature(obj = "tsRim")`: sets the m/z marker.

`rimStandard`

  `signature(obj = "tsRim")`: gets the standars.

`rimStandard<-`

  `signature(obj = "tsRim")`: sets the standars.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`ImportFameSettings`

### Examples

    showClass("tsRim")

    # create a rimLimit object:
    #  - set the lower (first column) and upper (second column) time limites to
    #    search for standards.
    Lim <- rbind(c(200, 300), c(400,450), c(600,650))
    #  - set the retention indices of the standard
    Std <- c(250000, 420000, 630000)
    #  - set the mass marker
    mass <- 87
    #  - create the object
    rimLimits <- new("tsRim", limits = Lim, standard = Std, mass = mass)

    # sometimes you need to change the limits of a particular standard
    rimLimits(rimLimits)[2,] <- c(410, 450)

    # to change the mass value
    rimMass(rimLimits) <- 85

    # to select a subset
    rim <- rimLimits[1:2]

    # remove a marker (number 3 in this case)
    rim <- rimLimits[-3]

[Package TargetSearch version 1.44.0 Index]