subset_mif: Subset mif object on cellular level

In spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

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)

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

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)

spatialTIME documentation built on June 22, 2024, 10:35 a.m.