specLSet-class {specL} | R Documentation

## Class `"specLSet"`

### Description

This class is used to store, show, and write generated results of the package.

### Objects from the Class

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

### Slots

`input.parameter`:

  A list of parameter values.

`ionlibrary`:

  A list of `"specL"` objects.

`rt.normalized`:

  A numeric vector of normalized retention time values.

`rt.input`:

  A numeric vector of retention time values.

### Methods

show

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

summary

  `signature(x = "specLSet")`: print summary of object content.

plot

  `signature(x = "specLSet")`: plots normalized versus input rt.

write.spectronaut

  `signature(x = "specLSet")`: writes object to ASCII file.

generate.consensus

  `signature(x = "specLSet")`: generates consensus specLSet object by combining all specL objects having a redundant group_id which is defined by `paste(x@q1.in_silico, x@peptideModSeq, sep='_')`.

merge.specLSet

  `signature(x = "specLSet")`: merges two specLSet objects.

ionlibrary

  `signature(x = "specLSet")`: returns a list of `specL` objects.

rt.input

  `signature(x = "specLSet")`: returns a numeric vector of input rt values.

rt.normalized

  `signature(x = "specLSet")`: returns a numeric vector of normalized rt values.

getProteinPeptideTable

  `signature(x = "specLSet")`: returns table of peptide protein mappings.

### Note

No notes yet.

### Author(s)

Christian Panse 2014

### See Also

`genSwathIonLib`

### Examples

        showClass("specL")
        showClass("specLSet")

[Package specL version 1.21.2 Index]