Spectral count for peptides and proteins in ProteinGroup objects.

Description

Spectral count for peptides and proteins in ProteinGroup objects. It can - other than spectra.count - quantify the spectra count on the level of peptides, potenitally modifed, too,

Usage

spectra.count2(ibspectra, value = reporterProteins(protein.group), 
               type = "protein.g", specificity = c("reporter-specific", "group-specific", "unspecific"), 
               modif = NULL, combine = FALSE, subset = NULL, require.quant = NULL, ...)

Arguments

Author(s)

Florian P Breitwieser

See Also

spectra.count, ProteinGroup

Examples

  data(ibspiked_set1)
  pg <- proteinGroup(ibspiked_set1)
  protein.gs <- protein.g(pg,"CERU")
  sc <- spectra.count2(ibspiked_set1,protein.gs)
  sc.ik <- spectra.count2(ibspiked_set1,protein.gs,modif="iTRAQ4plex_K")
  rbind(spectra.counts=sc,spectra.counts_iTRAQk=sc.ik)

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(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/spectra.count2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spectra.count2
> ### Title: Spectral count for peptides and proteins in ProteinGroup
> ###   objects.
> ### Aliases: spectra.count2
> 
> ### ** Examples
> 
>   data(ibspiked_set1)
>   pg <- proteinGroup(ibspiked_set1)
>   protein.gs <- protein.g(pg,"CERU")
>   sc <- spectra.count2(ibspiked_set1,protein.gs)
>   sc.ik <- spectra.count2(ibspiked_set1,protein.gs,modif="iTRAQ4plex_K")
>   rbind(spectra.counts=sc,spectra.counts_iTRAQk=sc.ik)
                      P00450 P13635 Q61147
spectra.counts           140    639    521
spectra.counts_iTRAQk     72    290    270
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>