R/chmi.08_list_names.R

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

#-----------------------------------
# CHMI list traits to re_classifing
#-----------------------------------


### all names traits in data------------------------------------------------------------------------

#' @export
chmi.all_names.class_vars <- function()
{
### traits
  all_names <- sort(c(
  	'allocation', 'analyte', 'antigen', 'batch', 'cell_population', 'chmi', 'comments',
  	'ct_marker', 'ct_value', 'cyto_pid', 'dataset', 'date', 'day_05', 'day_06', 'day_07', 'day_08',
  	'day_09', 'day_10', 'day_11', 'day_12', 'day_13', 'day_14', 'day_15', 'day_16', 'day_17',
  	'day_18', 'day_19', 'day_20', 'day_21', 'day_22', 'day_23', 'day_24', 'day_25', 'day_26',
  	'day_27', 'day_28', 'dil', 'dose', 'eos', 'esp', 'fc_log10_mfi', 'fc_mfic', 'fc_mfic_c1',
  	'gender', 'gr_hbs', 'gr2_hbs', 'group', 'hb', 'hb_status', 'height', 
  	'id_filter', 'immune_status', 'l1_malaria', 'label_point', 'leucos', 'log10_mfi', 'lymphos',
  	'mal_exposure', 'mal_pos', 'mean_ratio', 'mfi', 'mfi_adj', 'mfi_corr', 'mfi_imp',
  	'min_half', 'neutros', 'original_id', 'original_point_marker', 'pcr_pos', 'plate',
  	'platelets', 'ppp_mal', 'ppp_mal_rtqpcr', 'ppp_tbs', 'ppp_time', 'protection',
  	'route', 'rt_value', 'rt_value_c1', 'sample', 'status', 'study_number', 't_igg',
  	't_immuno', 't_point', 't2_malaria', 't2_parasit', 't2_point', 'tbs_pos', 'time',
  	'treatment', 'vaccine', 'weight'))
 
 
### factor variables with 'character' levels 	
 	lev_fact <- sort(c(
 		'allocation', 'analyte', 'antigen', 'batch', 'cell_population', 'ct_marker', 'cyto_pid',
 		'dataset', 'gender',  'gr_hbs', 'gr2_hbs', 'group', 'hb_status', 'id_filter', 
 		'immune_status', 'mal_exposure', 'plate',  'status', 't_igg', 't_immuno',
 		't_point', 't2_point', 'treatment', 'vaccine', 'cyto_pid', 'original_id', 
 		'original_point_marker', 'study_number', 'chmi', 'dil', 'dose', 'l1_malaria', 
 		'mal_pos', 'pcr_pos', 'protection', 'route', 'tbs_pos')) 
	 		
 
### character variables
	chr_vars <- sort(c('comments',  'esp'))
 
 
### double variables 	
	dbl_vars <- sort(c(
	 	'ct_value',  'eos', 'fc_log10_mfi', 'fc_mfic', 'fc_mfic_c1', 'hb', 'height', 'leucos',
	 	'log10_mfi', 'lymphos', 'mean_ratio', 'mfi', 'mfi_adj', 'mfi_corr', 'mfi_imp', 'min_half',
	 	'neutros', 'platelets', 'ppp_time',  'rt_value', 'rt_value_c1', 't2_malaria', 't2_parasit',
  	'weight'))
	 	

### integer variables
 	int_vars <- sort(c(
 	 	'day_05', 'day_06', 'day_07', 'day_08',
  	'day_09', 'day_10', 'day_11', 'day_12', 'day_13', 'day_14', 'day_15', 'day_16', 'day_17',
  	'day_18', 'day_19', 'day_20', 'day_21', 'day_22', 'day_23', 'day_24', 'day_25', 'day_26',
  	'day_27', 'day_28', 'ppp_mal', 'ppp_mal_rtqpcr', 'ppp_tbs'))


### date variables
  date_vars <- sort(c(
 	 	'date', 'time'))


l_names <- list(
	all_variables = all_names,
  factor_levels = lev_fact,
  character_vars = chr_vars,
  double_vars = dbl_vars,
  integer_vars = int_vars,
  date_vars = date_vars)

### return
  return(l_names)
}



### all names of antigen in 'ab_chmi'---------------------------------------------------------------

#' @export
chmi.all_names.class_ag_ab <- function()
{
### all analytes ('n == 30')
all_analyte <- c(
		'egf',  'eotaxin', 'fgf', 'g_csf', 'gmcsf', 'hgf', 'ifna', 'ifng', 
		'il10', 'il12', 'il13', 'il15', 'il17', 'il1b', 'il1ra', 'il2', 'il2r', 'il4', 'il5', 'il6', 
		'il7', 'il8',
		'ip10', 'mcp1', 'mig',  'mip1a', 'mip1b', 'rantes', 'tnfa', 'vegf')


### all antigens ('n == 23') 
	all_antigen <- c(
		'agal', 'ama1_3d71', 'ama1_fvo', 'bsa', 'cel_tos', 'csp', 'cy_rpa1', 'cy_rpa2', 'db_la',
		'eba175', 'exp1', 'lsa1', 'msp1_19', 'msp1_42_3d7', 'msp1_42_fvo', 'msp3', 'pf_aarp', 
		'pf_rh1', 'pf_rh2', 'pf_rh4', 'pf_rh5', 'ptramp', 'ssp2')

		
### all antigens ('n == 21') 
	ab_antigen <- c(
		'ama1_3d71', 'ama1_fvo', 'cel_tos', 'csp', 'cy_rpa1', 'cy_rpa2', 'db_la',
		'eba175', 'exp1', 'lsa1', 'msp1_19', 'msp1_42_3d7', 'msp1_42_fvo', 'msp3', 'pf_aarp',
		'pf_rh1', 'pf_rh2', 'pf_rh4', 'pf_rh5', 'ptramp', 'ssp2')


l_antigen <- list(
	cyto_analytes = all_analyte,
  ab_full = all_antigen,
  ab_select = ab_antigen)


### return
  return(l_antigen)
}