% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/debarcode_cytof.R
\name{debarcode_fcs}
\alias{debarcode_fcs}
\title{Main wrapper for the debarcoder pipeline.}
\usage{
debarcode_fcs(
  fcs,
  bc.key,
  output.dir,
  output.basename,
  sep.threshold,
  mahal.dist.threshold = 30
)
}
\arguments{
\item{fcs}{The input \code{flowFrame}}

\item{bc.key}{The barcode key, as returned by \code{read_barcode_key}}

\item{output.dir}{The output directory}

\item{output.basename}{The basename of the output files. For each debarcoded sample, the sample label will
be appended to this basename}

\item{sep.threshold}{The minimum seperation between the lowest barcode channel, and the highest non-barcode channel.
The data will be normalized before doing the assignments, therefore this number will typically be in \code{[0, 1]}}

\item{mahal.dist.threshold}{The maximum squared Mahalanobis distance between each event and the centroid
of the population that event has been assigned to. This is for further filtering the barcode assignments and it is not
always necessary. Events with distance above this threshold are left unassigned. The distance is capped at 30, therefore
the default value of this option corresponds to no filtering}
}
\value{
For each debarcoded sample, a new FCS file is created in the output directory. Unassigned events are written
 in a separate file
}
\description{
Takes all the parameters as input, does everything and writes back the FCS files
}
