merge_mifs: Merge several MIF objects together

In spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

Merge several MIF objects together

Description

This function merges MIF objects that were run separately so they can be used as a single MIF. MIF objects don't *need* but *should* have the same column names in the summary file and clinical data file. The MIF objects **DO** need to have the same patient_id and sample_id.

Usage

merge_mifs(mifs = NULL, check.names = T)

Arguments

mifs	A list of MIF objects to merge together
check.names	whether to check names of spatial files and summary enttries

Value

Returns a new MIF object list

clinical_data	clinical information from all
sample	cell level summary data from all
spatial	contains all spatial files from all MIFs
derived	appended derived variables
patient_id	patient_id from the first MIF - this is why it is important to have the same patient_id for all MIFs
sample_id	sample_id from the first MIF - also important for all MIFs to have the same sample_id

Examples

#merge several MIF objects
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")
x <- merge_mifs(mifs = list(x, x), check.names = FALSE)

spatialTIME documentation built on April 1, 2023, 12:18 a.m.