Data accompanying the Pbase package

Description

A small example Proteins test instance. This object is likely to change on a regular basis. It will be described more thoroughly when it becomes stable. The MSMS spectra that were searched against the database are available in the pms MSnExp object.

Usage

data(p)
data(pms)

See Also

The Pbase-data vignette.

Examples

data(p)
p
data(pms)
pms

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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/p.Rd_%03d_medium.png", width=480, height=480)
> ### Name: p
> ### Title: Data accompanying the 'Pbase' package
> ### Aliases: p pms
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(p)
> p
S4 class type     : Proteins
Class version     : 0.1
Created           : Sat Feb 14 12:36:40 2015
Number of Proteins: 9
Sequences:
  [1] A4UGR9 [2] A6H8Y1 ... [8] P04075-2 [9] P60709
Sequence features:
  [1] DB [2] AccessionNumber ... [12] npeps [13] ENST
Peptide features:
  [1] DB [2] AccessionNumber ... [27] acquisitionNum [28] filenames
> data(pms)
> pms
Object of class "MSnExp"
 Object size in memory: 4.79 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of MS1 acquisitions: 1 
 Number of MSn scans: 218 
 Number of precursor ions: 218 
 218 unique MZs
 Precursor MZ's: 401.88 - 1287.1 
 MSn M/Z range: 99.01 3813.78 
 MSn retention times: 16:32 - 48:60 minutes
- - - Processing information - - -
Data loaded: Sat Feb 14 12:37:09 2015 
 MSnbase version: 1.15.5 
- - - Meta data  - - -
phenoData
  rowNames: 1
  varLabels: sampleNames fileNumbers
  varMetadata: labelDescription
Loaded from:
  Thermo_Hela_PRTC_selected.mgf 
protocolData: none
featureData
  featureNames: X1 X10 ... X99 (218 total)
  fvarLabels: SCANS TITLE ... CHARGE (5 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>