Pparams-class {Pbase} | R Documentation

## Class `"Pparams"`

### Description

`Pbase` parametrisation infrastructure.

### Objects from the Class

New `Pbase` parameters can be generated with the `Pparams()` constructor. `Pparams` instances control various aspects of `Pbase` functions, as described in the Slots section below. If no parameters are passed to the respective functions, default values from `Pparams()` are used.

### Slots

`DbFormat`:

  The format of the protein sequence fasta database used to generate the `Proteins` object. Currently only `"UniProt"` is supported. `"RefSeq"` will be added as well as a mechanism to support arbitrary and custom fasta header.

`IdFormat`:

  The format of the identification data files used to add `pfeatures` to `Protein` instances. Currently, `mzIdentML` is supported.

`IdReader`:

  Package to be used to load the identification data. Currently one of `mzR` (via the `openIDfile` and `psms` functions) or `mzID` (via the `mzID` and `flatten` functions). Differences between these two architectures include the metadata available in the `Proteins`' `pfeatures`, speed and stability (`mzR` is much faster but less mature and currently susceptible to crashes).

`verbose`:

  A `logical` defining if the various functions display messages (default) or remain silent.

### Methods

show

  `signature(object = "Pparams")`: ...

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### Examples

    Pparams()
    Pparams(IdReader = "mzID")

    try(Pparams(IdReader = "mzid"))

[Package Pbase version 0.20.0 Index]