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

In fbreitwieser/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")

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.