create_mif: Create Multiplex Immunoflourescent object

In spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

Create Multiplex Immunoflourescent object

Description

Creates an MIF object for use in spatialIF functions

Usage

create_mif(
  clinical_data,
  sample_data,
  spatial_list = NULL,
  patient_id = "patient_id",
  sample_id = "image_tag"
)

Arguments

clinical_data	A data frame containing patient level data with one row per participant.
sample_data	A data frame containing sample level data with one row per sample. Should at a minimum contain a 2 columns: one for sample names and one for the corresponding patient name.
spatial_list	A named list of data frames with the spatial data from each sample making up each individual data frame
patient_id	A character string indicating the column name for patient id in sample and clinical data frames.
sample_id	A character string indicating the column name for sample id in the sample data frame

Value

Returns a custom MIF

clinical	Data frame of clinical data
sample	Data frame of sample data
spatial	Named list of spatial data
derived	List of data derived using the MIF object
patient_id	The column name for sample id in the sample data frame with the clinical data
sample_id	The column name for sample id in the sample data frame to merge with the spatial data

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")

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