Load and query CosMx/Xenium/Merscope transcript files as `arrow` datasets
GetTxData(
seurat = NULL,
features = NULL,
fovs = NULL,
cells = NULL,
tx_path = NULL
)a Seurat object containing Kandinsky data (`KanData()`)
character vector indicating genes/probes to select from the list of transcript. If `NULL`, no filter will be applied on genes/probes
character vector indicating the identifiers of fields of view (FOVs) of interest. If `NULL`, no filter will be applied on FOVs
character vector indicating the identifiers of the single cells of interest. If `NULL`, no filter will be applied on single cell identifiers
character string indicating the path for the transcript coordinates file from CoxMx/Xenium/Merscope platforms. If `NULL`, the function will expect to find the file path stored within the `tx` Kandinsky data slot
data frame containing the rows selected from the input transcript file
Transcript files are queried and filtered using `arrow` and `dplyr` functionalities to reduce the memory requirements even in the case of datasets with hundreds of millions of transcripts. In the current version, transcript files can be filtered according to cell identifiers, fov identifiers, and genes/probes of interest.