\name{calculate.emPAI}
\alias{calculate.emPAI}
\alias{n.observable.peptides}
\title{
  emPAI approximate abundance calculations.
}
\description{
  The Exponentially Modified Protein Abundance Index (emPAI) is a
  label free quantitative measure of protein abundance based on protein
  coverage by peptide matches. The original publication is 
  Ishihama Y, et al., Proteomics (2005).
}
\usage{
calculate.emPAI(protein.group, protein.g = reporterProteins(protein.group), ...)
n.observable.peptides(seq, nmc = 1, min.length = 6, min.mass = 800, max.mass = 4000, ...)
}
\arguments{
  \item{protein.group}{ProteinGroup object. Its \code{@proteinInfo}
    slot \code{data.frame} must contain a \code{sequence} column to
    calculate the number of observable peptides per protein.
  }
  \item{protein.g}{Protein group identifiers.}
  \item{seq}{Protein sequence.}
  \item{nmc}{Number of missed cleavages.}
  \item{min.length}{Minimum length of peptide.}
  \item{min.mass}{Minimum mass of peptide.}
  \item{max.mass}{Maximum mass of peptide.}
  \item{\dots}{Further arguments to \code{\link{n.observable.peptides}}/\code{\link[OrgMassSpecR]{Digest}}.}
}
\details{
  The formula is \deqn{emPAI = 10^{\frac{N <- {observed}}{N <- {observable}}} -1}{emPAI = 10^(N_observed/N_observable) -1}
  N_observed is the number of observed peptides - we use the count
  of unique peptide without consideration of charge state.
  N_observable is the number of observable peptides. 
  Sequence cleavage is done using \code{\link[OrgMassSpecR]{Digest}}.
}
\value{
  Named numeric vector of emPAI values.
}
\references{
  Ishihama Y, et al., Proteomics (2005)
}
\author{
  Florian P Breitwieser
}

\seealso{
  \code{\link[OrgMassSpecR]{Digest}},
  \code{\link{proteinInfo}},
  \code{\link{getProteinInfoFromUniprot}},
  \code{\link{calculate.dNSAF}},
  \code{\link{ProteinGroup}}
}
\examples{
data(ibspiked_set1)
protein.group <- proteinGroup(ibspiked_set1)
calculate.emPAI(protein.group,protein.g=protein.g(protein.group,"CERU"))
}
\keyword{ ~emPAI }