Read and Load Akoya CODEX data
ReadAkoya(
filename,
type = c("inform", "processor", "qupath"),
filter = "DAPI|Blank|Empty",
inform.quant = c("mean", "total", "min", "max", "std")
)LoadAkoya(
filename,
type = c("inform", "processor", "qupath"),
fov,
assay = "Akoya",
...
)
ReadAkoya
: A list with some combination of the following values
“matrix
”: a
sparse matrix with expression data; cells
are columns and features are rows
“centroids
”: a data frame with cell centroid
coordinates in three columns: “x”, “y”, and “cell”
“metadata
”: a data frame with cell-level meta data;
includes all columns in filename
that aren't in
“matrix
” or “centroids
”
When type
is “inform
”, additional expression matrices
are returned and named using their segmentation type (eg.
“nucleus”, “membrane”). The “Entire Cell” segmentation
type is returned in the “matrix
” entry of the list
LoadAkoya
: A Seurat
object
Path to matrix generated by upstream processing.
Specify which type matrix is being provided.
“processor
”: matrix generated by CODEX Processor
“inform
”: matrix generated by inForm
“qupath
”: matrix generated by QuPath
A pattern to filter features by; pass NA
to
skip feature filtering
When type
is “inform
”, the
quantification level to read in
Name to store FOV as
Name to store expression matrix as
Ignored
This function uses
progressr to
render status updates and progress bars. To enable progress updates, wrap
the function call in with_progress
or run
handlers(global = TRUE)
before running
this function. For more details about progressr, please read
vignette("progressr-intro")