% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/import.R

\name{importPhenoCycler}

\alias{importPhenoCycler}

\title{importPhenoCycler}

\usage{

importPhenoCycler(

  dir.path,

  assay_name = "PhenoCycler",

  sample_name = NULL,

  image_name = "main",

  type = c("inform", "processor", "qupath"),

  filter = "DAPI|Blank|Empty",

  inform.quant = c("mean", "total", "min", "max", "std"),

  verbose = TRUE,

  ...

)

}

\arguments{

\item{dir.path}{path to PhenoCycler output folder}

\item{assay_name}{the assay name of the SR object}

\item{sample_name}{the name of the sample}

\item{image_name}{the image name of the Xenium assay, Default: main}

\item{type}{Specify which type matrix is being provided.

\itemize{

 \item \dQuote{\code{processor}}: matrix generated by CODEX Processor

 \item \dQuote{\code{inform}}: matrix generated by inForm

 \item \dQuote{\code{qupath}}: matrix generated by QuPath

}}

\item{filter}{A pattern to filter features by; pass \code{NA} to skip feature filtering}

\item{inform.quant}{When \code{type} is \dQuote{\code{inform}}, the quantification level to read in}

\item{verbose}{verbose}

\item{...}{additional parameters passed to \link{formVoltRon}}

}

\description{

Importing PhenoCycler data

}