R/chmi.07_list_traits.R

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

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


### common traits in all data-----------------------------------------------------------------------

#' @export
chmi.l_traits.id <- function()
{
  # traits
  tr <- c('original_id', 'dataset')


  # list
  l_id <- list(
    traits = tr,
    description = c(as.character(chmi.l_traits.descriptions()[tr])),
    ranges_units = c(as.character(chmi.l_traits.units_ranges()[tr])))


  # return
  return(l_id)
}



### traits for '01_chmi_clinical' data--------------------------------------------------------------

#' @export
chmi.l_traits.clinical <- function()
{
  # traits
  tr_1 <- sort(c(
  	'gender', 'weight', 'height',
    'ppp_mal', 'ppp_time', 'ppp_tbs',
    't_immuno', 'immune_status', 'status', 'hb_status',
    'mal_pos', 'tbs_pos', 'pcr_pos',
    'group', 'dose', 'allocation',
    'chmi', 'protection', 'route', 't2_parasit',
    'ppp_mal_rtqpcr', 'vaccine', 'gr_hbs', 'gr2_hb', 'mal_exposure'))


	# traits for 'ab_data' and 'aim_1'
	aim_1 <- sort(c(
  	'gender', 'ppp_time', 'immune_status', 'status', 'mal_exposure'))


  # traits for 'ab_data' and 'aim_2'
	aim_2 <- sort(c(
  	'gender', 'ppp_time', 'immune_status', 'status', 'mal_exposure', 'vaccine'))


  # traits for 'ab_data' and 'aim_3'
	aim_3 <- sort(c(
  	'gender', 'ppp_time', 'status', 'mal_exposure', 'hb_status', 'gr_hbs', 'gr2_hbs'))


  # traits for 'ab_data' and 'aim_4'
	aim_4 <- sort(c(
  	'gender', 'ppp_time', 'status', 'hb_status', 'immune_status', 
  	'pcr_pos', 'tbs_pos', 'ppp_tbs', 't_immuno', 'mal_exposure'))
  	
 	
 	# traits for 'pbmc_data'
 	pbmc <- sort(c(
 		'gender', 'weight', 'height', 'status', 'hb_status', 'immune_status', 
  	'pcr_pos', 'tbs_pos', 'ppp_tbs', 'ppp_mal', 't_immuno'))
 		


  # list
  l_clin <- list(
    complete_tr = tr_1,
    tr_ab_aim_1 = aim_1,
    tr_ab_aim_2 = aim_2,
    tr_ab_aim_3 = aim_3,
    tr_ab_aim_4 = aim_4,
    tr_pbmc = pbmc,
    description = c(as.character(chmi.l_traits.descriptions()[tr_1])),
    ranges_units = c(as.character(chmi.l_traits.units_ranges()[tr_1])),
    source_files = c(as.character(chmi.l_traits.source_files()[tr_1])))


  # return
  return(l_clin)
}



### traits for '01_chmi_ab' data--------------------------------------------------------------------

#' @export
chmi.l_traits.ab <- function()
{
	# traits
	tr_1 <- sort(c(
		't_igg', 'antigen', 'study_number', 't_point', 'plate', 'batch',
		'mfi',	'min_half', 'mfi_imp', 'dil', 'mfi_adj', 'mean_ratio', 'mfi_corr', 'log10_mfi',
		't2_point'))


	tr_2 <- sort(c(
		't_igg', 'antigen', 't_point', 't2_point', 'mfi_corr', 'log10_mfi'))


	# list
  l_ab <- list(
    complete_tr = tr_1,
    select_tr = tr_2,
    description = c(as.character(chmi.l_traits.descriptions()[tr_1])),
    ranges_units = c(as.character(chmi.l_traits.units_ranges()[tr_1])))


  # return
  return(l_ab)
}



### traits for '04_chmi_pbmc' data------------------------------------------------------------------

#' @export
chmi.l_traits.pbmc <- function()
{
  # traits
  tr_1 <- sort(c(
  	't_point', 't2_point', 'date', 'ct_marker', 'cell_population', 'ct_value', 'fact_marker'))


  # list
  l_pbmc <- list(
    complete_tr = tr_1,
    description = c(as.character(chmi.l_traits.descriptions()[tr_1])),
    ranges_units = c(as.character(chmi.l_traits.units_ranges()[tr_1])))


  # return
  return(l_pbmc)
}