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Marker Frequency Difference

Source: R/marker_freq_diff.R
marker_freq_diff.Rd

marker_freq_diff allows users to easily calculate the difference in marker abundance (frequency) between different tissue compartments. For us this is typically looking at tumor vs stroma marker abundance.

Usage

marker_freq_diff(
  mif,
  classifier,
  ref_level,
  diff_level,
  mnames,
  overwrite = FALSE
)

Arguments

mif

object of class mif created with create_mif()

classifier

character that specified which column in the spatial data indicates the different tissue compartments profiled

ref_level

character found in the classifier column of spatial data indicating the first value when calculating frequency difference

diff_level

character found in the classifier column of spatial data indicating the second value when calculating frequency difference

mnames

character vector of marker names that are found in the spatial data for which to calculate abundance differences

overwrite

boolean/logical for whether to overwrite previously calculated marker frequency differences

Value

an object of class mif with the derived$frequency_difference slot filled

Details

To calculate a p-value associated with the difference in proportion of positive markers identified in different classifier compartments, we implemented the use of the Fisher's Exact test.

Examples

mif <- create_mif(clinical_data = example_clinical %>% 
                                 dplyr::mutate(deidentified_id = as.character(deidentified_id)),
                               sample_data = example_summary %>% 
                                 dplyr::mutate(deidentified_id = as.character(deidentified_id)),
                               spatial_list = example_spatial,
                               patient_id = "deidentified_id", 
                               sample_id = "deidentified_sample")
mif = marker_freq_diff(mif = mif,
                       classifier = "Classifier.Label",
                       ref_level = "Tumor", 
                       diff_level = "Stroma",
                       mnames = c("CD3..FOXP3.", "CD3..CD8.", "CD3..PD1.", "CD3..PD.L1.",
                                  "CD3..Opal.570..Positive", "PD1..Opal.650..Positive"),
                       overwrite = TRUE)