R/remove_samples.R

In ChristofSeiler/CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

#' Remove samples based on low cell counts
#'
#' @param df_samples_subset Data frame or tibble with proteins counts,
#'   cell condition, and group information
#' @param condition The column name of the condition variable
#' @param group The column name of the group variable
#' @param unpaired true if unpaired samples were provided as input
#' @param cell_n_min Remove samples that are below this cell counts threshold
#' @return NULL.
#'
remove_samples <- function(df_samples_subset,
                           condition,
                           group,
                           unpaired,
                           cell_n_min) {

  cell_count <- table(pull(df_samples_subset,group),
                     pull(df_samples_subset,condition))
  include <- NULL
  if(cell_n_min < Inf) {
    if(unpaired) {
      exclude <- which(rowSums(cell_count) < cell_n_min)
    } else {
      exclude <- which(apply(cell_count,1,min) < cell_n_min)
    }
    include <- rownames(cell_count)[!rownames(cell_count) %in% names(exclude)]
  } else {
    include <- rownames(cell_count)
  }
  df_samples_subset[pull(df_samples_subset,group) %in% include,] %>%
    droplevels()

}