This function takes the information from the molecules and boundaries slot, and counts the molecules per region of interest. Its input is a MoleculeExperiment object, and its output a SpatialExperiment object. That way, if one is interested in doing downstream analyses at the cell level, one can do so.
Usage
countMolecules(
me,
moleculesAssay = "detected",
boundariesAssay = "cell",
buffer = 0,
matrixOnly = FALSE,
nCores = 1
)Arguments
- me
MoleculeExperiment object containing both the transcript data as well as the boundaries data. I.e., the "molecules" and "boundaries" slots need to be filled. See MoleculeExperiment() for more information.
- moleculesAssay
Character string naming the list of the molecules slot from which transcript information should be retrieved from. The default is the detected transcript data that is read in when creating a MoleculeExperiment object. It is possible to change it to another mode, e.g., "high_threshold" will access the transcript information that has been stored in the "high_threshold" element of the list in the molecules slot.
- boundariesAssay
Character string naming the list of the boundaries slot from which boundary information should be retrieved from. For example, for counting transcripts per cell, the list containing the cell boundaries (e.g., "cell") should be selected.
- buffer
Single numeric value (default 0) indicating value to buffer beyond segment boundaries, i.e. to count molecules just outside of a segment boundary
- matrixOnly
Logical value indicating whether to return a matrix of the counted molecules per segment (e.g., cell). Is FALSE by default, i.e., the default output is a SpatialExperiment object.
- nCores
Number of cores to use for the operation.
Value
A SpatialExperiment object derived from a MoleculeExperiment object. Alternatively, a matrix with the counted molecules per segment.
Examples
repoDir <- system.file("extdata", package = "MoleculeExperiment")
repoDir <- paste0(repoDir, "/xenium_V1_FF_Mouse_Brain")
me <- readXenium(repoDir,
keepCols = "essential"
)
spe <- countMolecules(me)
spe
#> class: SpatialExperiment
#> dim: 178 14
#> metadata(0):
#> assays(1): counts
#> rownames(178): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2
#> rowData names(0):
#> colnames(14): sample1.67500 sample1.67512 ... sample2.65070
#> sample2.65071
#> colData names(4): sample_id cell_id x_location y_location
#> reducedDimNames(1): spatial
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x_location y_location
#> imgData names(0):