MasterPeptides-class {synapter} | R Documentation

## Class `"MasterPeptides"`

### Description

A class to store the results of `makeMaster`. This class stored the 2 versions (orders) of the master final peptide data.

### Objects from the Class

Objects can be created by calls of the form `makeMaster`.

### Slots

`masters`:

  Object of class `"list"` storing the 2 master `data.frame` objects.

`pepfiles`:

  Object of class `"character"` with the list of final peptide input files.

`fdr`:

  Object of class `"numeric"` with the peptide false discovery applied when creating the filter.

`method`:

  Object of class `"character"` with the peptide p-value adjustment method. One of `BH` (default), `qval` or `Bonferroni`.

`orders`:

  Object of class `"list"` with the `numeric` vectors specifying the order of `pepfiles` used to generate the respective `masters` `data.frames`.

`fragmentfiles`:

  Object of class `"character"` with the list of final fragment input files.

`fragments`:

  Object of class `data.frame` storing the combined final fragment data.

`fragmentlibrary`:

  Object of class `"MSnExp"` storing the fragment library.

### Methods

show

  `signature(object = "MasterPeptides")`: to print a textual representation of the instance.

### Author(s)

Laurent Gatto

### References

Improving qualitative and quantitative performance for MSE-based label free proteomics, N.J. Bond, P.V. Shliaha, K.S. Lilley and L. Gatto, Journal of Proteome Research, 2013, in press.

The Effects of Travelling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies, P.V. Shliaha, N.J. Bond, L. Gatto and K.S. Lilley, Journal of Proteome Research, 2013, in press.

[Package synapter version 2.18.0 Index]