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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Pbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Rcpp
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.12.2

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Pbase/Pparams-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Pparams-class
> ### Title: Class '"Pparams"'
> ### Aliases: Pparams-class Pparams show,Pparams-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> Pparams()
DbFormat: UniProt; IdFormat: mzid; IdReader: mzR; verbose: TRUE
> Pparams(IdReader = "mzID")
DbFormat: UniProt; IdFormat: mzid; IdReader: mzID; verbose: TRUE
> 
> try(Pparams(IdReader = "mzid"))
Error in match.arg(IdReader) : 'arg' should be one of "mzR", "mzID"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>