R/chmi.01_phen.update_dat_imp.R

In mvazquezs/chmitools: Package to manage & obtain results of the CHMI Study

#--------------------
# Update `chmi.phen`
#--------------------



### update 'dat_imp'--------------------------------------------------------------------------------
chmi.update_phenos.dat_imp <- function(dat_imp)
{
### update all list of 'dat_imp'
	for(i in 2:length(dat_imp)) {
		dat_imp[[i]] <- dat_imp[[i]] %>%
			clean_names(case = 'old_janitor') %>%
	 	 	remove_empty(which = 'cols') %>%
	 	 	mutate(
	 	 		t2_point = as.character(case_when(
      		c(dataset == 'L1' & t_point == 'D13') ~ 'D11_D13',
	    		c(dataset == 'L1' & t_point == 'D5') ~ 'D7',
      		c(dataset %in% c('L1', 'T1', 'T2') & t_point %in% c('D11', 'DM')) ~ 'D11_D13',
     			TRUE ~ as.character(t_point))))

	}

### update only in '02_chmi_ab'
	dat_imp[[2]] <- dat_imp[[2]] %>%
		mutate(
			log10_mfi = as.numeric(log10(mfi_corr)))


### update only in '03_chmi_cyto'
	dat_imp[[3]] <- dat_imp[[3]] %>%
		clean_names(case = 'old_janitor') %>%
		mutate(
			plate = factor(paste0('plate0', plate),
				levels = c(sprintf('plate0%d', seq(1:max(plate)))))) %>%
		pivot_longer(
  		cols = fgf:il8,
  		names_to = 'analyte',
  		values_to = 'log10_mfi')


### update only in '04_chmi_pbmc'
	dat_imp[[4]] <- dat_imp[[4]] %>%
		pivot_longer(
  		cols = vbc_cd10:mzb_cd1c_no_igm,
  		names_to = 'cell_population',
  		values_to = 'ct_value')


### return
	return(dat_imp)
}