R/check_data.R

In tidymass/masscleaner: Data cleaning for LC-MS based metabolomics data

#' @title check_for_qc_normalization
#' @description check_for_qc_normalization
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param object mass_dataset
#' @return error information
#' @export

check_for_qc_normalization <-
  function(object) {
    ###QC samples
    if (all(unique(object@sample_info$class) != "QC")) {
      return("error: No QC samples in object, please check and see here: 
             https://tidymass.github.io/masscleaner/articles/error_no_subject_qc.html")
      
    }
    
    if (all(unique(object@sample_info$class) != "Subject")) {
      return("error: No Subject samples in object, please check and see here:
             https://tidymass.github.io/masscleaner/articles/error_no_subject_qc.html")
    }
    
    ##injection.order
    if (all(colnames(object@sample_info) != "injection.order")) {
      return("error: No injection.order samples in object, please check.")
    }
    
    ###has batch or not
    if (all(colnames(object@sample_info) != "batch")) {
      object@sample_info$batch <- 1
    }
    
    # if (any(is.na(object@sample_info$batch))) {
    #   return("error: NA is in batch from sample_info, please check.")
    # }
    
    ###check injection.order information
    sample_info <-
      object@sample_info
    
    ###remove blank samples
    sample_info <-
      sample_info %>% 
      dplyr::filter(!is.na(injection.order))
    
    purrr::map(
      unique(sample_info$batch),
      .f = function(batch_idx) {
        temp_sample_info <-
          sample_info %>%
          dplyr::filter(batch == batch_idx)
        
        qc_order <- temp_sample_info %>%
          dplyr::filter(class == "QC") %>%
          dplyr::pull(injection.order)
        
        if (min(qc_order) != 1) {
          return(paste("error: batch", batch_idx, "QC injection order is not from 1"))
        }
        
        if (max(qc_order) != max(sample_info$injection.order)) {
          return(paste(
            "error: batch",
            batch_idx,
            "QC injection order is not end last one"
          ))
        }
      }
    )
    return("ok")
  }





#' @title check_for_data_integration
#' @description check_for_data_integration
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param object mass_dataset
#' @param method method for integrate_data
#' @return error information
#' @export

check_for_data_integration <-
  function(object,
           method = c("qc_mean",
                      "qc_median",
                      "subject_mean",
                      "subject_median")) {
    method <- match.arg(method)
    
    ###batch
    if (all(colnames(object@sample_info) != "batch")) {
      return("warning: No batch information in object.")
    } else{
      if (length(unique(object@sample_info$batch)) == 1) {
        return("warning: only one batch.")
      }
    }
    
    ###QC samples
    if (method == "qc_mean" |
        method == "qc_median") {
      if (all(unique(object@sample_info$class) != "QC")) {
        return("error: No QC samples in object.")
      }
      
      purrr::map(
        unique(object@sample_info$batch),
        .f = function(temp_batch) {
          number <-
            object@sample_info %>%
            dplyr::filter(batch == temp_batch & class == "QC") %>%
            nrow()
          if (number == 0) {
            return(paste("error: batch", temp_batch, "has no QC."))
          }
        }
      )
    }
    
    
    ###Subject samples
    if (method == "subject_mean" |
        method == "subject_median") {
      if (all(unique(object@sample_info$class) != "Subject")) {
        return("error: No Subject samples in object.")
      }
      
      purrr::map(
        unique(object@sample_info$batch),
        .f = function(temp_batch) {
          number <-
            object@sample_info %>%
            dplyr::filter(batch == temp_batch &
                            class == "Subject") %>%
            nrow()
          if (number == 0) {
            return(paste("error: batch", temp_batch, "has no Subject"))
          }
        }
      )
    }
    
    return("ok")
    
  }