spatialTIME (version 1.3.4-4)

subset_mif: Subset mif object on cellular level

Description

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)

Value

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

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

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)