peptide.count: Peptide counts, spectral counts and sequence coverage for...

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

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

See Also

calculate.emPAI, calculate.dNSAF, ProteinGroup

Examples

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

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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 1.22.0)
   '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

isobar documentation built on Nov. 8, 2020, 7:48 p.m.