Simple function for extracting metadata from he DeepBlue server in R

extracting_metadata.R

deepblue_extract_metadata <- function(epi_mark,epi_project, auth_key) {
  
  #get sample ids
  experiments_ids <- deepblue_list_experiments(epigenetic_mark = epi_mark,
                                               project = epi_project,
                                               user_key = auth_key)
  
  #extracting all information
  metadata <- deepblue_info(deepblue_extract_ids(experiments_ids), user_key = auth_key)
  
  #making the data.frame
  metadata_df <- unique(foreach(sample = metadata,
                                 .combine = bind_rows,
                                 .inorder = TRUE) %do% {
                                   meta <- as.data.frame(sample$sample_info)
                                   meta$epigenetic_mark <- sample$epigenetic_mark
                                   meta$data_type <- sample$data_type
                                   meta$genome <- sample$genome
                                   meta$experiment <- sample$name
                                   meta$technique <- sample$technique
                                   meta <- cbind(meta, sample$extra_metadata)
                                   return(meta)
                                 })
  return(metadata_df)
}