isobar (version 1.18.0)

peptide.count: 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

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")