create_mif {spatialTIME}

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")