Pparams-class: Class '"Pparams"'

In ComputationalProteomicsUnit/Pbase: Manipulating and exploring protein and proteomics data

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 <[e-mail]>

Examples

Pparams()
Pparams(IdReader = "mzID")

try(Pparams(IdReader = "mzid"))

ComputationalProteomicsUnit/Pbase documentation built on Aug. 10, 2019, 1:25 a.m.