% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{pancreasSCE}
\alias{pancreasSCE}
\title{Example SingleCellExperiment object}
\format{
A SingleCellExperiment object containing the raw and
arcsinh-transformed mean pixel counts per cell as well as associated cell-
and protein-specific metadata. Row names represent the names of the target
proteins and column names represent the image name and cell id of each cell.
\describe{
\item{colData}{Cell-specific metadata where rownames represent the
image name and cell id. It containins the
\enumerate{
    \item image number (ImageNb),
    \item cell number/identifier (CellNb),
    \item spatial position on the image (Pos_X, Pos_Y),
    \item the associated image name (ImageName, see
    \code{?"\link[cytomapper]{pancreasImages}"}),
    \item the associated mask name (MaskName, see
    \code{?"\link[cytomapper]{pancreasMasks}"}),
    \item a arbitrary cell-type label (CellType)
    \item a logical (Pattern) indicating exocrine cells
}
}
\item{rowData}{Protein-specific metadata where rownames represent
the names of the target proteins. It contains the
\enumerate{
    \item channel number (frame),
    \item metal tag of the antibody (MetalTag)
    \item Target (the expanded name of the targeted protein)
    \item clean_Target (the abbreviated name of the targeted protein)
}
}
\item{assays}{List of protein expression counts containing:
\enumerate{
\item the raw expression counts (counts):
mean pixel value per cell and protein
\item arcsinh-transformed raw expression counts
using a co-factor of 1 (exprs)
}
}
}
}
\usage{
pancreasSCE
}
\description{
This \linkS4class{SingleCellExperiment} object contains the expression values
of 5 proteins (rows) from 362 cells (columns) across 3 images. The data is
part of a imaging mass cytometry study on the progression of Type 1 diabetes
and therefore contains pancreas cells.
}
\references{
\href{https://www.sciencedirect.com/science/article/pii/S1550413118306910}{
Damond, N. et al., A Map of Human Type 1 Diabetes Progression by
Imaging Mass Cytometry, Cell Metabolism 29:3, 2019}
}
\keyword{datasets}