MIDTOD

R code for MIDTOD

Dependencies and requirements

• R (>3.6.0)
• Input MS files must be generated by MarkerView and R package artMS
• Text file of a table of significantly regulated genes

Usage

The MIDTOD software will identify metabolites.

Test on Example Data

To test and run on example data, download the full repository as a zip archive from Code menu above or (click here)

Unzip the archive. Open a command line terminal and set the new MIDTOD directory as you working directory. The first line below sets the working directory (and is appropriate for most Mac OSX), you will have to edit the path to the unzipped MIDTOD directory on your computer. The next set of lines is a single command that runs MIDTOD on data files in the example/ subdirectory. On completion you should see numerous output files in example/output/

cd ~/Downloads/MIDTOD-master/

Rscript metabolomics_pipeline.R \
             -f example/shortened.H5N1_Mouse_Lung_results-wide.txt \
             -e example/shortened.H5N1_Mouse_Lung_evidence.txt \
             -s mouse \
             -o example/output/ \
             -x example/shortened.otherOmicsData.txt

More help

Minimum command:

Rscript metabolomics_pipeline.R -f (results_file) -e (evidence_file) -x (orthogonal data file)

arguments

arguments:
f=results [f]ile
e=[e]vidence file
o=[o]utput directory
s=[s]pecies
  accepted values: human, mouse
x=orthogonal data file
m=[m]ode: positive or negative.  The expected charge on the metabolites in MS

More help at the command line

Rscript metabolomics_pipeline.R --help

Power users

For full control, run within R:

source ("midtod.R", chdir=TRUE)

outDir <- "example/output/"
dir.create (outDir, recursive = TRUE, showWarnings = FALSE)

midtod(resultsFile  = "example/shortened.H5N1_Mouse_Lung_results-wide.txt",
       evidenceFile = "example/shortened.H5N1_Mouse_Lung_evidence.txt",
       outputDir    = outDir,
       species      = "mouse",
       remove.infinites = FALSE,
       orthogonalDataFile = "example/shortened.otherOmicsData.txt",
       log2FC = 1,
       pvalue = 0.05,
       filterResult = FALSE,
       mode = "positive"
       )

Generating input files with artMS

See artMS help for instructions on generating an evidence file (section 7.1) and a results file (section 7.3) that is suitable for input to MIDTOD:

https://www.bioconductor.org/packages/devel/bioc/vignettes/artMS/inst/doc/artMS_vignette.html#7_METABOLOMICS

Orthogonal omics data format

MIDTOD relies on detected regulation at genes in known pathways via other omics to identify regulated metabolites in metabolomics data. This other omics data is supplied to MIDTOD via a table in tab separated format with the following column names. See file example/shortened.otherOmicsData.txt for a full example.

  experiment_id
  omics_type
  condition_2
  cell_line
  strain
  entrez_id
  symbol
  q_value
  log2fc