% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/QC.R
\name{SpaceTrooper-deprecated}
\alias{SpaceTrooper-deprecated}
\alias{computeQCScore}
\alias{computeQCScoreFlags}
\alias{computeOutliersQCScore}
\alias{applyQCScoreModel}
\title{Deprecated functions in SpaceTrooper}
\usage{
computeQCScore(spe, bestLambda = NULL, modelFormula = NULL, verbose = FALSE)

computeQCScoreFlags(spe, qsThreshold = 0.5, useQSQuantiles = FALSE)

computeOutliersQCScore(
  spe,
  metricList = c("log2SignalDensity", "Area_um", "log2AspectRatio",
    "log2Ctrl_total_ratio")
)

applyQCScoreModel(spe, qcModel, scoreName = "QC_score")
}
\arguments{
\item{spe}{A `SpatialExperiment` object with QC metrics already computed.}

\item{bestLambda}{Passed to \code{\link{computeQScore}}.}

\item{modelFormula}{Passed to \code{\link{computeQScore}}.}

\item{verbose}{Passed to \code{\link{computeQScore}}.}

\item{qsThreshold}{Passed to \code{\link{computeQScoreFlags}}.}

\item{useQSQuantiles}{Passed to \code{\link{computeQScoreFlags}}.}

\item{metricList}{Passed to \code{\link{computeOutliersQScore}}.}

\item{qcModel}{A historical QC score model object, usually stored in
`metadata(spe)$QCScore_model`.}

\item{scoreName}{Name of the legacy output column in `colData`.}
}
\value{
A `SpatialExperiment` object; see \code{\link{computeQScore}}.

A `SpatialExperiment` object; see \code{\link{computeQScoreFlags}}.

A `SpatialExperiment` object; see
  \code{\link{computeOutliersQScore}}.

A `SpatialExperiment` object with the applied score in `colData`
  and the model in `metadata(spe)$QCScore_model_applied`.
}
\description{
These functions are retained for compatibility with published SpaceTrooper
APIs. They issue a deprecation warning and direct users to the canonical
Quality Score functions.
}
\details{
\itemize{
  \item `computeQCScore()` replaces canonical `QScore` and
    `metadata(spe)$QScore_model` with historical `QC_score` and
    `metadata(spe)$QCScore_model`.
  \item `computeQCScoreFlags()` consumes `QC_score` and creates
    `low_qcscore` and, when applicable, `low_threshold_qcscore`.
  \item `computeOutliersQCScore()` is the historical name for
    `computeOutliersQScore()`.
  \item `applyQCScoreModel()` retains the `qcModel` argument, the default
    `QC_score` output, and `metadata(spe)$QCScore_model_applied`.
}

Use `computeQScore()`, `computeQScoreFlags()`,
`computeOutliersQScore()`, and `applyQScoreModel()` for canonical names.
}
