Read NanoString CosMx SMI output into a SpaCET object.
Usage
create.SpaCET.object.CosMx(cosmxPath, fov = NULL, organism = "human")
Arguments
- cosmxPath
Path to the CosMx output folder containing the expression matrix and metadata.
- fov
Field of view indices to include. Default NULL loads all FOVs.
- organism
Species, either "human" (default) or "mouse".
Examples
if (FALSE) { # \dontrun{
SpaCET_obj <- create.SpaCET.object.CosMx(cosmxPath = "/path/to/cosmx_output")
} # }