R/mhs.luminex.R

In phoebehlam/fhrc: provide fhrc lab with different r scripts

#' consolidate luminex output for mhs only
#'
#' consolidate mfi and cv from individual outputs
#' 
#' @param path the folder to which all the individual files are saved
#' @examples
#' mhs.luminex (path= "/Users/phoebelam/Box/FHRC/Mentoring & Health Study (MHS)/Wet Lab/Immunoassays/Luminex/Cohort 1 Data")
#'
#' 
#' @importFrom magrittr "%>%"
#' @export
mhs.luminex <- function(path) {
  
  filenames = list.files(path=path, pattern = ".xlsx" ,full.names= TRUE, recursive=FALSE)
  
  consol <- data.frame(matrix(ncol = 1, nrow = 1))
  saveRDS(consol, paste(path,"/consolidated.RDS", sep=""))
  
  for (f in filenames) {
    
    print(f)
    
    # dilution factor
    # dil <- xlsx::read.xlsx("/Users/phoebelam/Desktop/mhs/MHS Cohort 1 102-117 V1 102-115 V2_20200303_142229_TABS.xlsx",
    #                        sheetName = "Raw Data")

    dil <- xlsx::read.xlsx(f, sheetName = "Raw Data")
    which(dil$NA. == "Dilution Factor")+1 -> start
    which(dil$xPONENT=="Analysis Types")-1 -> end
    dil[start:end,] %>%
      dplyr::select(xPONENT, NA.) %>%
      dplyr::rename(Sample = xPONENT,
                    dilution = NA.) %>%
      dplyr::distinct(Sample, .keep_all = T) %>%
      dplyr::filter(!(grepl("Standard|Background|CNTR|CTR|TM|EMPTY", Sample)==T))-> dil
    
    # cv
    # cvdat <- xlsx::read.xlsx("/Users/phoebelam/Desktop/mhs/MHS Cohort 1 102-117 V1 102-115 V2_20200303_142229_TABS.xlsx",,
    #                          sheetName = "%CV Replicates", startRow = 2)
    
    cvdat <- xlsx::read.xlsx(f, sheetName = "%CV Replicates",startRow = 2)
    cvdat %>%
      dplyr::select(Sample,IL.8,IL.1b,IL.6,TNF.a) %>%
      dplyr::rename (il8.cv = IL.8,
                     il1b.cv = IL.1b,
                     il6.cv = IL.6,
                     tnfa.cv = TNF.a) %>%
      dplyr::select(Sample, il8.cv, il1b.cv, il6.cv, tnfa.cv) %>% 
      dplyr::mutate(filename.cv=basename(f)) %>%
      dplyr::filter(!(grepl("Standard|CTR|EMPTY", Sample)==T) & is.na(Sample)==F) -> cvdat
    
    # mfi values
    # mfidat <- xlsx::read.xlsx("/Users/phoebelam/Desktop/mhs/MHS Cohort 1 102-117 V1 102-115 V2_20200303_142229_TABS.xlsx",
    #                           sheetName = "Avg Net MFI", startRow = 2)

    mfidat <- xlsx::read.xlsx(f, sheetName = "Avg Net MFI",startRow = 2)
    mfidat %>%
      dplyr::select(Sample:TNF.a) %>%
      dplyr::filter(is.na(Sample) == FALSE & grepl("Standard", Sample)==F) %>% 
      dplyr::select(Sample, IL.8,IL.1b,IL.6,TNF.a) %>%
      dplyr::rename(il8 = IL.8,
                    il1b = IL.1b,
                    il6 = IL.6,
                    tnfa = TNF.a) %>% 
      dplyr::mutate(filename.mfi=basename(f)) %>%
      dplyr::filter(!(grepl("Standard|CTR|EMPTY", Sample)==T) & is.na(Sample)==F) ->mfidat
    
    #merge
    pecan::mergethem(mfidat, cvdat, dil) -> together
    
    consol <- readRDS(paste(path,"/consolidated.RDS", sep=""))
    consol <- gtools::smartbind(consol,together)
    saveRDS(consol, paste(path,"/consolidated.RDS", sep=""))

  }
  
  write.csv(consol, paste(path, "/mhs_long_", Sys.Date(), ".csv", sep=""), row.names=F, na="")
  
  

}