Read and Load Akoya CODEX data

Source: R/preprocessing.R, R/convenience.R

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",
  ...
)

Arguments

filename

Path to matrix generated by upstream processing.

type

Specify which type matrix is being provided.

  • “processor”: matrix generated by CODEX Processor

  • “inform”: matrix generated by inForm

  • “qupath”: matrix generated by QuPath

filter

A pattern to filter features by; pass NA to skip feature filtering

inform.quant

When type is “inform”, the quantification level to read in

fov

Name to store FOV as

assay

Name to store expression matrix as

...

Ignored

Value

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

Note

This function requires the data.table package to be installed

Progress Updates with progressr

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")