--- a +++ b/man/importPhenoCycler.Rd @@ -0,0 +1,45 @@ +% 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 +}