R/chmi.03_phen.argument_clinical_tr.R

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

#-------------------------------------
# chmi.03_phen.argument_clinical_tr.R
#-------------------------------------


### argument to update 'aim_ab_data' and 'fold_change'----------------------------------------------

chmi.03_phen.argument_clinical_tr <- function(data_type, aim_data)
{
### argument 'aim_data'
	if(data_type == 'ab_data' & aim_data == 'aim_1') {
	# aim_1
		l_vars <- c(
			chmi.l_traits.id()[['traits']],
			chmi.l_traits.clinical()[['tr_ab_aim_1']])
				
	} else if(data_type == 'ab_data' & aim_data == 'aim_2') {
	# aim_2
		l_vars <- c(
			chmi.l_traits.id()[['traits']],
			chmi.l_traits.clinical()[['tr_ab_aim_2']])

 	} else if(data_type == 'ab_data' & aim_data == 'aim_3') {
	# aim_3
		l_vars <- c(
			chmi.l_traits.id()[['traits']],
			chmi.l_traits.clinical()[['tr_ab_aim_3']])
	
	} else if(data_type == 'ab_data' & aim_data == 'aim_4') {
	# aim_4
		l_vars <- c(
			chmi.l_traits.id()[['traits']],
			chmi.l_traits.clinical()[['tr_ab_aim_4']])
	
	} else if (data_type == 'pbmc_data' & aim_data == 'none') {
	# pbmc data_type
				l_vars <- c(
				chmi.l_traits.id()[['traits']],
				chmi.l_traits.clinical()[['tr_pbmc']])
	
	} else if (data_type %nin% c('ab_data', 'pbmc_data') & aim_data == 'none') {
		# complete traits
		l_vars <- c(
			chmi.l_traits.id()[['traits']],
			chmi.l_traits.clinical()[['complete_tr']])
	}


### return
	return(l_vars)
}