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
Either a named list of data frames with the spatial data from each sample making up each individual data frame, or a named character vector of paths to parquet files, one sample per file, which builds a disk-backed mif that reads each sample only when a computation needs it. The files are referenced where they are and never copied or modified. Use this for whole slide images, where holding every sample in memory at once is what stops a multi-core run from starting – see
mif_to_disk()for the sizes involved and for building a store from data already in memory. If the vector is unnamed, names are taken from each file'ssample_idcolumn.- 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")