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Last data update: 2014.03.03

R: Peptide counts, spectral counts and sequence coverage for...

peptide.count

R Documentation

Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.

Description

Report the peptide count, spectral count and sequence coverage for supplied proteins.

Usage

peptide.count(protein.group, protein.g = reporterProteins(protein.group), 
              specificity = c("reporter-specific", "group-specific", "unspecific"), ...)

spectra.count(protein.group, protein.g = reporterProteins(protein.group), 
              specificity = c("reporter-specific", "group-specific", "unspecific"), 
              modif = NULL, ...)

sequence.coverage(protein.group, protein.g = reporterProteins(protein.group), 
                  specificity = c("reporter-specific", "group-specific", "unspecific"), 
                  simplify = TRUE, ...)

Arguments

`protein.group`	ProteinGroup object.
`protein.g`	Protein group identifier.
`specificity`	Specificity of peptides.
`modif`	Only count peptides having a certain modification.
`simplify`	If simplify=TRUE, a named numeric vector is returned, with the mean sequence coverage of the ACs of each protein.g supplied. Else, a list with the length of protein.g is returned having the sequence coverage for each protein AC.
`...`	Further arguments to `peptides`

Author(s)

Florian P Breitwieser

Examples

  data(ibspiked_set1)
  sc <- spectra.count(proteinGroup(ibspiked_set1))
  pc <- peptide.count(proteinGroup(ibspiked_set1)) 
  plot(jitter(sc),jitter(pc),log="xy")

Results


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> 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/peptide.count.Rd_%03d_medium.png", width=480, height=480)
> ### Name: peptide.count
> ### Title: Peptide counts, spectral counts and sequence coverage for
> ###   ProteinGroup objects.
> ### Aliases: peptide.count spectra.count sequence.coverage
> 
> ### ** Examples
> 
>   data(ibspiked_set1)
>   sc <- spectra.count(proteinGroup(ibspiked_set1))
>   pc <- peptide.count(proteinGroup(ibspiked_set1)) 
>   plot(jitter(sc),jitter(pc),log="xy")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>