R/report_missing.R

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

report_missing <- function(dat,
                           input_col,
                           report_col,
                           verbose=TRUE){
  report_missing_i <- function(dat,
                               input_col,
                               report_col,
                               verbose=TRUE){
    phenos2 <- dat[,c(input_col,report_col),with=FALSE] |> unique()
    n_missing <- sum(is.na(phenos2[[report_col]]))
    n_total <- nrow(phenos2)
    messager(formatC(n_missing,big.mark = ","),
             "/",
             formatC(n_total,big.mark=","),
             paste0("(",round(n_missing/n_total*100,2),"%)"),
             report_col,"missing.",v=verbose)
  }
  for(rc in report_col){
    report_missing_i(dat = dat,
                     input_col = input_col,
                     report_col = rc,
                     verbose = verbose)
  }
}