Isobar Data packages

Description

ibspiked_set1 and ibspiked_set2 are objects of class iTRAQ4plexSpectra. It contains over 160 protein groups, over 1600 peptides from about 15,000 spectra each, mainly from background proteins and three spiked-in Ceruplasmins (CERU_HUMAN, CERU_MOUSE, CERU_RAT).

Usage

  data(ibspiked_set1)
  data(ibspiked_set2)
  data(ib_phospho)

Format

iTRAQ4plexSpectra objects.

Source

isobar publication. Acquired on Orbitrap instrument w/ 20 offline-fractions and HCD fragmentation.

Examples

data(ibspiked_set1)
print(ibspiked_set1)

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.
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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(isobar)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to isobar (v 1.18.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    paste0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isobar/isobar-data.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isobar.data
> ### Title: Isobar Data packages
> ### Aliases: ibspiked_set1 ibspiked_set2 noise.model.hcd ib_phospho
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ibspiked_set1)
> print(ibspiked_set1)
iTRAQ4plexSpectra (storageMode: lockedEnvironment)
assayData: 14991 features, 4 samples 
  element names: ions, mass 
protocolData: none
phenoData: none
featureData
  featureNames: M261-D07-HS-P1948-1.1765.1765.2.dta.38373
    M261-C07-HS-P1948-1.2376.2376.3.dta.26320 ...
    M261-D06-HS-P1948-1.1660.1660.3.dta.37304 (14991 total)
  fvarLabels: peptide modif ... use.for.quant (12 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
14991  spectra
ProteinGroup object
    1653 peptides are detected
     157 protein groups with specific peptides
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>