specL-class {specL} | R Documentation

## Class `"specL"`

### Description

This class is used to store, print, and plot the generated results of the package.

### Objects from the Class

Objects can be created by calls of the form `new("specL", ...)`.

### Slots

`group_id`:

  Object of class `"character"` just an id

`peptide_sequence`:

  Object of class `"character"` AA sequence

`proteinInformation`:

  Object of class `"character"` a string contains the protein identifier.

`q1`:

  Object of class `"numeric"` peptide weight m/Z as measured by the MS device

`q1.in_silico`:

  Object of class `"numeric"` peptide weight m/Z computed in-silico.

`q3`:

  Object of class `"numeric"` measured fragment ions.

`q3.in_silico`:

  Object of class `"numeric"` in-silico derived fragment ions.

`score`:

  Object of class `"numeric"` taken from bibliospec - psm score

`prec_z`:

  Object of class `"numeric"` pre-cursor charge.

`frg_type`:

  Object of class `"character"` fragmenbt ion type, e.g., b or y ion.

`frg_nr`:

  Object of class `"numeric"` fragment ion number

`frg_z`:

  Object of class `"numeric"` fragment ion charge.

`relativeFragmentIntensity`:

  Object of class `"numeric"` percentage base peaks of frament ions.

`irt`:

  Object of class `"numeric"` independent retention time in seconds.

`peptideModSeq`:

  Object of class `"numeric"` a vector contains the mass diff between AA and mod AA.

`mZ.error`:

  Object of class `"numeric"` a string contains the protein identifier.

`filename`:

  Object of class `"character"` a string contains the filename of the ions.

### Methods

plot

  `signature(x = "specL")`: plots the fragment ions of `specL` object.

show

  `signature(x = "specL")`: shows the content of `specL` object.

write.spectronaut

  `signature(x = "specL")`: writes the `specL` object to a ASCII file.

### Note

No notes yet.

### Author(s)

Christian Panse 2014

### See Also

`genSwathIonLib`

### Examples

        showClass("specL")

[Package specL version 1.14.0 Index]