% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_mzid.R
\name{tdc_qvalues}
\alias{tdc_qvalues}
\title{Compute monotone q-values by target-decoy counting (internal)}
\usage{
tdc_qvalues(score, is_decoy, add_decoy = 1L)
}
\arguments{
\item{score}{Numeric vector. Higher is better.}

\item{is_decoy}{Logical vector. TRUE=decoy, FALSE=target.}

\item{add_decoy}{Integer scalar. FDR hat = (D + add_decoy) / T.}
}
\value{
Numeric vector of q-values in \verb{[0,1]}.
}
\description{
Computes FDR estimates along the score-sorted list and returns monotone q-values:
\eqn{q(i) = \min_{j \ge i} \widehat{FDR}(j)}.
}
\keyword{internal}
