convert MDS ELISA data to Prism ready format

convert_MDS_to_Prism.r

install.packages(c("tidyverse", "janitor", "readxl"))
library(tidyverse)
library(janitor)
library(readxl)

convert_MDS_to_Prism<- function(infile_path, sheet_range, outfile_path){
        
        if (!file.exists(infile_path)){
                stop("the input file does not exist, please check your file name!")
        }
        
        data<- map(sheet_range, function(x) readxl::read_xlsx(infile_path, x, skip = 1)) %>%
        bind_rows( .id = "sheet") %>%
        janitor::clean_names() %>% 
        mutate(calc_concentration = str_replace(calc_concentration, "NaN", NA_character_)) %>%
        mutate(calc_concentration = as.numeric(calc_concentration)) %>%
        group_by(sheet, sample, assay) %>%
        summarise(mean_conc = mean(calc_concentration, na.rm =TRUE)) %>%
        pivot_wider(names_from = c(assay, sheet), values_from = mean_conc) %>%
        janitor::clean_names() %>%
        select(sample, order(colnames(.))) 
        
        write_csv(data, file = outfile_path)
        message(paste0("please find the converted file at ", outfile_path))
                
}



infile<- "C:\\Users\\AlexandriaFusco\\Downloads\\CRS Data 06132022 Soluble Plate Data Record 08162022.xlsx"

outfile<- "C:\\Users\\AlexandriaFusco\\Downloads\\CRS Data 06132022 Soluble Plate Data Record 08162022.csv"

sheet_range<- 1:3

convert_MDS_to_Prism(infile_path = infile, sheet_range = sheet_range, outfile_path = outfile)