pancreasSCE | R Documentation |
This 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.
pancreasSCE
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.
Cell-specific metadata where rownames represent the image name and cell id. It containins the
image number (ImageNb),
cell number/identifier (CellNb),
spatial position on the image (Pos_X, Pos_Y),
the associated image name (ImageName, see
?"pancreasImages"
),
the associated mask name (MaskName, see
?"pancreasMasks"
),
a arbitrary cell-type label (CellType)
a logical (Pattern) indicating exocrine cells
Protein-specific metadata where rownames represent the names of the target proteins. It contains the
channel number (frame),
metal tag of the antibody (MetalTag)
Target (the expanded name of the targeted protein)
clean_Target (the abbreviated name of the targeted protein)
List of protein expression counts containing:
the raw expression counts (counts): mean pixel value per cell and protein
arcsinh-transformed raw expression counts using a co-factor of 1 (exprs)
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