average_marker_intensity_within_radius

Source: R/average_marker_intensity_within_radius.R

Calculates the average intensity of the target_marker within a radius from the cells positive for the reference marker. Note that it pools all cells with the target marker that are within the specific radius of any reference cell. Results represent the average intensities within a radius, but do not correspond to metrics for each cell

average_marker_intensity_within_radius(
  sce_object,
  reference_marker,
  target_marker,
  radius = 20
)

Arguments

sce_object

A SingleCellExperiment object in the form of the output of format_image_to_sce
reference_marker

A string specifying the marker that is used for reference cells
target_marker

A string specifying the marker to calculate its average intensity
radius

An integer specifying the radius of search for cells around the reference cells

Value

A single number is returned

Examples

average_marker_intensity_within_radius(SPIAT::formatted_image,
                                       reference_marker ="CD8",
                                       target_marker = "CD4",
                                       radius=30)

#> [1] 10.13677