R/gen_metadata.R

In anishchakka/gmeta: Generates metadata

#' Generate metadata as S4 object
#'
#' This function converts metadata dataframes to S4 object. It assumes that the format
#' as generated by gen_sample_sheets() in gmeta package. It requires both archr and sample
#' metadata dataframes.
#'
#' @param archr_meta archR readme dataframe.
#' @param sample_meta sample metadata sheet.
#' @return S4 object of the two dataframes.
#' @examples
#' gen_meta_obj(archr_meta, sample_meta)
#' @export
gen_meta_obj <- function(archr_meta, sample_meta) {
  setClass("archr",
           slots = list(point.person = "character",
                        date = "character",
                        notes = "character",
                        taxonomy = "character",
                        metric = "vector",
                        threshold = "vector",
                        batch = "vector",
                        study = "character",
                        load = "vector",
                        cells.prefilter = "character",
                        cells.postfilter = "character"))

  setMethod("show",
            "archr",
            function(object) {
              cat("point.person:",object@point.person, "\n")
              cat("date:",object@date, "\n")
              cat("notes:", object@notes, "\n")
              cat("taxonomy:", object@taxonomy, "\n")
              cat("metric:", object@metric, "\n")
              cat("batch:", object@batch, "\n")
              cat("study:", object@study, "\n")
              cat("load:", object@load, "\n")
              cat("cells.prefilter:", object@cells.prefilter, "\n")
              cat("cells.postfilter:", object@cells.postfilter, "\n")
            })

  archr.obj <- new("archr",
                      point.person = archr_meta$Point_person,
                      date = archr$Date,
                      notes = archr_meta$Notes,
                      taxonomy = archr_meta$Taxonomy,
                      metric = archr_meta$Metric,
                      threshold = archr_meta$Threshold,
                      batch = archr_meta$Batch,
                      study = archr_meta$Study,
                      load = archr_meta$Load,
                      cells.prefilter = archr_meta$Cell_PreFilter,
                      cells.postfilter = archr_meta$Cell_PostFilter)

  meta.obj <- list(sample.metadata = sample_meta, archR = archr.obj)

  return(meta.obj)
}

#' get metadata sample sheets in the right format
#'
#' @return sample_metadata.txt and archr_metadata.txt files
#' @examples
#' gen_sample_sheets()
#' @export
gen_sample_sheets <- function() {
  sample.meta <- data.frame(matrix(vector(),ncol=7))
  colnames(sample.meta) <-c("Studies", "Batch_vendor_name", "Load_name", "Donor_name", "Age", "Sex", "ROI")
  write.table(sample.meta, file = "sample_metadata.txt", quote = FALSE, sep = "\t", row.names = FALSE)

  archr_meta <- data.frame(matrix(vector(),ncol=11))
  colnames(archr_meta) <-c("Point_person", "Date", "Notes", "Taxonomy",
                           "Metric", "Threshold", "Batch", "Study", "Load",
                           "Cell_PreFilter", "Cell_PostFilter")
  write.table(archr_meta, file = "archr_metadata.txt", quote = FALSE, sep = "\t", row.names = FALSE)

}