\name{peptide.count}
\alias{peptide.count}
\alias{spectra.count}
\title{
  Peptide and spectral counts for ProteinGroup objects.
}
\description{
  Reports the peptide and spectral count 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"))
}
\arguments{
  \item{protein.group}{ProteinGroup object.}
  \item{protein.g}{Protein group identifier.}
  \item{specificity}{Specificity of peptides.}
}
\author{
  Florian P Breitwieser
}

\seealso{
  \code{\link{calculate.emPAI}},
  \code{\link{calculate.dNSAF}},
  \code{\link{ProteinGroup}}
}
\examples{
  data(ibspiked_set1)
  sc <- spectra.count(proteinGroup(ibspiked_set1))
  pc <- peptide.count(proteinGroup(ibspiked_set1)) 
  plot(jitter(sc),jitter(pc),log="xy")
}