Serum Incubation Experiments Analysis

Summary

This tool helps perform data analysis by producing line charts detailing trends of WT, Serum, QC and Strains, based on results obtained from Compound Discoverer 3.1, after conducting LCMS Analysis.

Usage

The entry point for the analysis is the controller.R file

The following setings have to be provided, in the controller.R file

• Input files

  The user has to provide the following file paths required in the analysis

  • Positive and Negative results files
  • Positive and Negative run order files

  These are specified in the controller.R as;

    NEGATIVE_RESULTS_FILE = ""
    NEGATIVE_RUN_ORDER_FILE = ""
  
    POSITIVE_RESULTS_FILE = ""
    POSITIVE_RUN_ORDER_FILE = ""
  

  The input files are expected to be comma separated CSV files

• Input file parameters

  Specify the first and last columns with Strain, WT, Serum data. The 1st column is usually the 1st column after MS2. Column numbers start with 1

  Example

    NEGATIVE_RESULT_FIRST_COLUMN = 28
    NEGATIVE_RESULT_LAST_COLUMN = 140
    POSITIVE_RESULT_FIRST_COLUMN = 28
    POSITIVE_RESULT_LAST_COLUMN = 142
  

• Output files

  Specify the following output files;

    # file to hold intermediate data after preprocessing, before rendering charts
    OUTPUT_DATA_FILE = "data.rda"
    # CSV file with intermediate data from RMD rendering to be used for further analysis
    OUTPUT_CSV_FILE = "data.csv"
    # file for rendered html output
    OUTPUT_HTML_FILE = "output.html"
  

• Working directory

  The entry program will need to reference other packages in the common folder. The appropriate working directory should thus be set;

    # set the appropriate working directory
    setwd(".")