Subset mif object on cellular level — subset

This function allows to subset the mif object into compartments. For instance a mif object includes all cells and the desired analysis is based on only the tumor or stroma compartment then this function will subset the spatial list to just the cells in the desired compartment

Usage

subset_mif(mif, classifier, level, markers, path = NULL)

Arguments

mif: An MIF object
classifier: Column name for spatial dataframe to subset
level: Determines which level of the classifier to keep.
markers: vector of
path: for a disk-backed mif only (see mif_to_disk()), the directory to write the subset store to. Required in that case and ignored otherwise: the subset of a cohort too large for memory is generally also too large for memory, so it is written out sample by sample rather than returned in one piece.

Value

mif object where the spatial list only as the cell that are the specified level.

Examples

#' #Create mif object
library(dplyr)
x <- create_mif(clinical_data = example_clinical %>% 
mutate(deidentified_id = as.character(deidentified_id)),
sample_data = example_summary %>% 
mutate(deidentified_id = as.character(deidentified_id)),
spatial_list = example_spatial,
patient_id = "deidentified_id", 
sample_id = "deidentified_sample")

markers = c("CD3..Opal.570..Positive","CD8..Opal.520..Positive",
"FOXP3..Opal.620..Positive","PDL1..Opal.540..Positive",
"PD1..Opal.650..Positive","CD3..CD8.","CD3..FOXP3.")

mif_tumor = subset_mif(mif = x, classifier = 'Classifier.Label', 
level = 'Tumor', markers = markers)