R/detect_format.R

In sritchie73/ukbnmr: Removal of Unwanted Technical Variation from UK Biobank NMR Metabolomics Biomarker Data

detect_format <- function(x, type) {
  # Silence CRAN NOTES about undefined global variables (columns in data.tables)
  UKB.Field.ID <- QC.Flag.Field.ID <- NULL

  if (type == "biomarkers") {
    field_ids <- ukbnmr::nmr_info[, na.omit(UKB.Field.ID)]
  } else if (type == "biomarker_qc_flags") {
    field_ids <- ukbnmr::nmr_info[, na.omit(QC.Flag.Field.ID)]
  } else if (type == "sample_qc_flags") {
    field_ids <- ukbnmr::sample_qc_info$UKB.Field.ID
  } else {
    stop("internal error: 'type' must be one of \"biomarkers\", \"biomarker_qc_flags\", or \"sample_qc_flags\"")
  }

  raw_ukb_cols <- c(paste0(field_ids, "-0.0"), paste0(field_ids, "-1.0"))
  ukbtools_cols <- c(paste0(field_ids, "_0_0"), paste0(field_ids, "_1_0"))
  ukbconv_r_cols <- c(paste0("f.", field_ids, ".0.0"), paste0("f.", field_ids, ".1.0"))
  ukb_rap_cols <- c(paste0("p", field_ids, "_i0"), paste0("p", field_ids, "_i1"))
  if (!is.data.frame(x)) {
    stop("Input data must be a data.frame or data.table")
  }
  if (type != "sample_qc_flags" & length(intersect(names(x), ukbnmr::nmr_info[["Biomarker"]])) > 0) {
    return("processed")
  } else if (type == "sample_qc_flags" & length(intersect(names(x), ukbnmr::sample_qc_info[["Name"]])) > 0) {
    return("processed")
  } else if (length(intersect(names(x), raw_ukb_cols)) > 0) {
    return("raw")
  } else if (length(intersect(gsub(".*_f", "", names(x)), ukbtools_cols)) > 0) {
    return("ukbtools")
  } else if (length(intersect(names(x), ukbconv_r_cols)) > 0) {
    return("ukbconv_r")
  } else if (length(intersect(names(x), ukb_rap_cols)) > 0) {
    return("ukb_rap")
  } else {
    if (type == "biomarkers") {
      stop("NMR biomarker fields (#23400-23648) not found in input data")
    } else if (type == "biomarker_qc_flags") {
      stop("NMR biomarker QC Flag fields (#23700-23948) not found in input data")
    } else if (type == "sample_qc_flags") {
      stop("NMR sample QC Flag fields (#23649-23660) not found in input data")
    } else {
      stop("internal error: 'type' must be one of \"biomarkers\", \"biomarker_qc_flags\", or \"sample_qc_flags\"")
    }
  }
}