R/preprocess_pheno_geneva.R

In FernandoMarcon/REbola: Reproducible Ebola Vaccine Research

#' Preprocess Geneva Pheno Data
#'
#' @param pheno
#' @param print_schema
#'
#' @return
#' @export
#'
#' @examples
preprocess_pheno_geneva <- function(pheno, print_schema=F){
  #--> TODO
  # !!! Need to either encode to M-Male/F-Female as character, or transform this into FACTOR
  # for now I'll put as factor

  # Library Batch & Volunteer ID: need to be encoded as character, otherwise either numeric or factor type would attribute
  # order/magnitude to the sequenctial numbers

  # Missing Values
  schema = list(
    'numeric' = c('Dose','Group Day','Age','Mapped Reads','Sampling Day','On Target'),
    'character' = c('Sample','Gender','Library Batch','Volunteer ID'),
    'float' = c('Viremia','Fever'),
    'factor' = c('Treatment','Artrithis','Chills','Myalgia','OBJ Fever','Pain','Subj Fever','Viremia D1')
  )

  if(print_schema) print(schema)

  # Numeric Vars
  pheno$Dose = sapply(gsub('x','*',gsub('Placebo','0',pheno$Dose)), function(x) eval(parse(text=x)))
  pheno = pheno %>% dplyr::mutate( Dose = as.numeric(gsub(',','.',Dose)),
                                   `Group Day` = as.numeric(gsub('X','', `Group Day`)),
                                   Age = as.numeric(Age),
                                   `Mapped Reads` = as.numeric(`Mapped Reads`),
                                   `Sampling Day` = as.numeric(`Sampling Day`),
                                   `On Target` = as.numeric(gsub(',','.',`On Target`))
  )

  # Character Vars
  pheno <- pheno %>% dplyr::mutate(
    Gender = as.factor(Gender),
    Sample = paste0('S',Sample),
    `Library Batch` = as.character(`Library Batch`),
    `Volunteer ID` = as.character(`Volunteer ID`)
  )

  # Float Vars
  pheno <- pheno %>% dplyr::mutate(  Fever = as.numeric(gsub(',','.',Fever)),
                                     Viremia = as.numeric(gsub(',','.',Viremia)))

  # Factor Variables
  factor_vars = schema[[ 'factor' ]]
  pheno[,factor_vars] = lapply(pheno[,factor_vars], as.factor)

  # pheno = pheno %>% setNames(tolower(gsub("\\.","_",names(.)))) %>% rename(sample_id = sample)
  colnames(pheno) <- gsub(" |\\.", "_", colnames(pheno))
  colnames(pheno) <- tolower(colnames(pheno))
  colnames(pheno)[which(colnames(pheno) == "sample")] <- "sample_id"
  return(pheno)
}