R/chmi.02_phen.argument_data_type.R

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

#-----------------------------------
# chmi.02_phen.argument_data_type.R
#-----------------------------------


### join 'ab_data' and 'none'-----------------------------------------------------------------------

chmi.02_phen.argument_ab_data <- function(dat_imp)
{
### ensure 69 individuals into 'antibodies' CHMI study
	l_ab_id <- c(
		chmi.id.ab_in()[['lachmi']],
		chmi.id.ab_in()[['tuchmi_1']],
		chmi.id.ab_in()[['tuchmi_2']])
		
		
	dat_imp[[1]] <- dat_imp[[1]] %>%
		filter(original_id %in% l_ab_id)

### ensure 21 antigen selected into 'antibodies' CHMI study
	l_ab_selected <- chmi.all_names.class_ag_ab()[['ab_select']]

	dat_imp[[2]] <- dat_imp[[2]] %>%
		filter(antigen %in% l_ab_selected) %>%
		droplevels()
	
### list of dataset to join
	l_ab_dat <- dat_imp[c(1:2)]


### 'reduce()' and 'left_join()'
dat <- l_ab_dat %>%
	reduce(left_join, by = c('original_id', 'dataset')) 


### return
	return(dat)
}



### join 'cyto_data' and 'none'---------------------------------------------------------------------

chmi.02_phen.argument_cyto_data <- function(dat_imp)
{
### ensure 69 individuals into 'antibodies' CHMI study
	l_cyto_id <- c(
		chmi.id.cyto_in()[['lachmi']],
		chmi.id.cyto_in()[['tuchmi_1']],
		chmi.id.cyto_in()[['tuchmi_2']])
	
	dat_imp[[1]] <- dat_imp[[1]] %>%
		filter(original_id %in% l_cyto_id)
		

### list of dataset to join
	l_cyto_dat <- dat_imp[c(1, 3)]

		
### 'reduce()' and 'left_join()'
dat <- l_cyto_dat %>%
	reduce(left_join, by = c('original_id', 'dataset')) 


### return
	return(dat)
}


### join 'pbmc_data' and 'none'---------------------------------------------------------------------

chmi.02_phen.argument_pbmc_data <- function(dat_imp)
{
### ensure 55 individuals into 'antibodies' CHMI study
	l_pbmc_id <- c(
		chmi.id.pbmc_in()[['lachmi']],
		chmi.id.pbmc_in()[['tuchmi_1']],
		chmi.id.pbmc_in()[['tuchmi_2']])
	
	dat_imp[[1]] <- dat_imp[[1]] %>%
		filter(original_id %in% l_pbmc_id)
		

### list of dataset to join
	l_pbmc_dat <- dat_imp[c(1, 4)]

		
### 'reduce()' and 'left_join()'
dat <- l_pbmc_dat %>%
	reduce(left_join, by = c('original_id', 'dataset')) 

### return
	return(dat)
}


### join 'pbmc_data' and 'none'---------------------------------------------------------------------

chmi.02_phen.argument_hemo_data <- function(dat_imp)
{
### ensure 28 individuals into 'antibodies' CHMI study
	l_hemo_id <- c(
		chmi.id.hemo_in()[['lachmi']])
	
	dat_imp[[1]] <- dat_imp[[1]] %>%
		filter(original_id %in% l_hemo_id)
		

### list of dataset to join
	l_hemo_dat <- dat_imp[c(1, 5)]

		
### 'reduce()' and 'left_join()'
dat <- l_hemo_dat %>%
	reduce(left_join, by = c('original_id', 'dataset', 'treatment')) 

### return
	return(dat)
}