R/parseBSD.R

In RGLab/R2i: Tools for preparing an ImmPort Data Submission

# helper for subsetting
subsetBSD <- function(tblName, bsdDF) {
  blanks <- grep("^$", bsdDF[[1]])
  startLn <- grep(paste0("^", tblName, "$"), bsdDF[[1]]) + 1

  if (tblName != "study_pubmed") {
    endLn <- blanks[blanks > startLn][[1]] - 1
  } else {
    endLn <- nrow(bsdDF)
  }

  subDF <- data.frame(bsdDF[startLn:endLn, ], stringsAsFactors = F)

  if (tblName == "study") {
    subDF <- subDF[, !(grepl("^V", colnames(subDF)))]
    subDF <- data.frame(t(subDF), stringsAsFactors = F)
    rownames(subDF) <- NULL
    colnames(subDF) <- subDF[1, ]
    subDF <- subDF[-1, ]
  } else if (tblName == "study_2_protocol") {
    subDF <- data.frame(
      `Protocol ID` = c(subDF[1, 2]),
      stringsAsFactors = FALSE,
      check.names = FALSE
    )
  } else {
    colnames(subDF) <- subDF[1, ]
    subDF <- subDF[-1, ]
    subDF <- subDF[, !(grepl("^$|\\.", colnames(subDF)))]
  }

  attr(subDF, "templateName") <- tblName # Important for checkTemplate()!

  return(subDF)
}


#' @title parse the basic study design template and return a list of R data frames
#'
#' @description function parses a csv version of the basic study design template
#'     from ImmPort to generate a list of R data frames that can then be checked with
#'     the quality control functions in the package.
#'
#' @param filePath file path for basic study design csv. Cannot be excel spreadsheet.
#' @importFrom utils read.csv read.table
#' @importFrom data.table fread
#' @export
parseBSD <- function(filePath) {
  # read in csv, txt
  type <- tools::file_ext(filePath)
  if (type == "txt") {
    bsdDF <- read.table(filePath, fill = T, stringsAsFactors = F, sep = "\t")
  } else if (type == "csv") {
    bsdDF <- read.csv(filePath, fill = T, stringsAsFactors = F)
  } else {
    stop("File extension unrecognized.  Must be either txt or csv.")
  }


  # break up into segments and generate return object
  tbls <- c(
    "study",
    "arm_or_cohort",
    "inclusion_exclusion",
    "planned_visit",
    "study_2_protocol",
    "study_file",
    "study_link",
    "study_personnel",
    "study_pubmed"
  )

  res <- sapply(tbls, subsetBSD, bsdDF = bsdDF)
}