R/fetch_bridging_control.R

In qiuyugong-aifi/QCBATCH: This packages is used to perform QC of bacth effect

#' Title
#'
#' @return
#' @export
#'
#' @examples
fetch_bridging_control <- function() {
  filter_list <- list(
    sample.bridgingControl = "true"
  )

  rna_desc_IMM <- getFileDescriptors(
    fileType = "scRNA-seq-labeled",
    filter = filter_list
  )
  rna_desc_IMM <- fileDescToDataframe_beta(rna_desc_IMM)

  selected_IMM <- cacheFiles(list(rna_desc_IMM$file.id))
  rna_desc_IMM <- fileDescToDataframe(selected_IMM)


  # fetch info for bridging control samples
  # some bridging control dataset missing some pattern,so cannot be fetched through HISE instance, have to do it manually
  fres2 <- hise::readFiles(list(
    "d96cfdea-1017-4ec0-b737-8fe87a24d486", "13f76644-0ba2-41e3-9075-d1035e6e5b98", "fe3393eb-c6f0-46a7-b70e-f42bd1e13611",
    "edc63d4e-6feb-4169-ae69-37d6bdb1691d", "8a5a1463-721f-4618-87f5-cc2c4185a311", "1290ac85-40a1-479e-bf1d-f2eacf941aa5",
    "6c2dea7e-870b-46a1-a356-99821567fdf3", "0d2b8c64-70d7-4990-8f03-05330c98d006", "50cec494-7deb-475a-b97e-cac27d38df4b",
    "76c91c6a-fa94-4c93-a70a-b3e326756b8a", "e4bab562-4ab5-4df8-8491-3603ac8587e4", "816495b0-73a6-4419-8314-2e704d696be1",
    "69d367f3-ae46-4e0c-b2ba-556ecc9af770"
  ))
  # get meta data info for this spefific batch
  meta_data_control <- NULL
  for (i in 1:length(fres2)) {
    desc <- unlist(fres2[[i]]$descriptors)
    desc <- desc[!grepl("scheme", names(desc))]
    names(desc) <- sub("^descriptors.", "", names(desc))

    desc <- as.list(desc)
    desc$labDisplay.version <- NULL
    df <- as.data.frame(desc)

    meta_data_control <- rbind(meta_data_control, df)
  }
  file_path <- NULL
  file_pool <- NULL
  for (i in 1:length(fres2)) {
    file_path <- c(file_path, paste0("cache/", meta_data_control$file.id[i], "/", tail(str_split(meta_data_control$file.name[i], "/")[[1]], n = 1)[1]))
    file_pool <- c(file_pool, substr(str_split(rna_desc_IMM$file.name[i], "/")[[1]][length(str_split(rna_desc_IMM$file.name[i], "/")[[1]])], 6, 7))
  }

  meta_data_control$filePath <- file_path
  meta_data_control$file_pool <- file_pool
  meta_data_control$file_keep <- paste0(meta_data_control$file.batchID, "-", meta_data_control$file_pool)


  # fetch info for bridging control samples
  # add additional info into data frame
  file_path <- NULL
  file_pool <- NULL
  for (i in 1:dim(rna_desc_IMM)[1]) {
    file_path <- c(file_path, paste0("cache/", rna_desc_IMM$file.id[i], "/", str_split(rna_desc_IMM$file.name[i], "/")[1][[1]][6]))
    file_pool <- c(file_pool, substr(str_split(rna_desc_IMM$file.name[i], "/")[[1]][length(str_split(rna_desc_IMM$file.name[i], "/")[[1]])], 6, 7))
  }
  rna_desc_IMM$file_pool <- file_pool
  rna_desc_IMM$file_keep <- paste0(rna_desc_IMM$file.batchID, "-", rna_desc_IMM$file_pool)


  rna_desc_IMM <- rbind(rna_desc_IMM, meta_data_control[c(colnames(rna_desc_IMM))])

  duplicated <- rna_desc_IMM %>% find_duplicates(file_keep)
  duplicated <- duplicated[order(duplicated$file_keep), ]

  filepath_to_delete <- c()
  for (i in 1:dim(duplicated)[1]) {
    single_sample <- duplicated %>% filter(file_keep == duplicated[i, ]$file_keep)
    filepath <- single_sample$filePath
    time <- c()
    for (z in filepath) {
      time <- c(time, str_split(str_split(z, "_")[[1]][4], "T")[[1]][1])
    }
    single_sample$time <- time
    filepath_to_delete <- c(filepath_to_delete, single_sample[single_sample$time == min(single_sample$time), ]$filePath)
  }
  filepath_to_delete <- unique(filepath_to_delete)
  rna_desc_IMM <- rna_desc_IMM %>% dplyr::filter(!filePath %in% filepath_to_delete)

  return(rna_desc_IMM)
}