MotrpacBicQC: Metabolomics QC

Expected submission

The folder/file structure of a required metabolomics submission is as follows:

Example:

PASS1A-06/
  T55/
   HILICPOS/ 
    metadata-phase.txt  ## Note: "new" required file
    file_manifest_YYYYMMDD.txt
    BATCH1_20190725/ 
     RAW/
      Manifest.txt
      file1.raw
      file2.raw
      etc
    PROCESSED_20190725/
     metadata_failedsamples_[cas_specific_labeling].txt
     NAMED/
        results_metabolites_named_[cas_specific_labeling].txt 
        metadata_metabolites_named_[cas_specific_labeling].txt
        metadata_sample_named_[cas_specific_labeling].txt
        metadata_experimentalDetails_named_[cas_specific_labeling].txt
     UNNAMED/ ## Note: Only required for untargeted assays
        results_metabolites_unnamed_[cas_specific_labeling].txt
        metadata_metabolites_unnamed_[cas_specific_labeling].txt
        metadata_sample_unnamed_[cas_specific_labeling].txt
        metadata_experimentalDetails_unnamed_[cas_specific_labeling].txt

With the following file relations…

Install MotrpacBicQC

First, download and install R and RStudio:

• R
• RStudio (free version)

Then, open RStudio and install the devtools package

install.packages("devtools")

Finally, install the MotrpacBicQC package. Important: install it every time that you run the QCs to ensure that the latest version is used.

library(devtools)
devtools::install_github("MoTrPAC/MotrpacBicQC", build_vignettes = FALSE)

Usage

Load the library

library(MotrpacBicQC)

And run any of the following tests to check that the package is correctly installed and it works. For example:

# Just copy and paste in the RStudio terminal

check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named")
check_metadata_samples(df = metadata_sample_named, cas = "umichigan")
check_results(r_m = results_named, m_s = metadata_sample_named, m_m = metadata_metabolites_named)

which should generate the following output:

check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named")

##   + (+) All required columns present

##   + (+) `metabolite_name` OK

##   + (+) `refmet_name` unique values: OK

##   + Validating `refmet_name` (it might take some time)

##       (-) `refmet_name` [`Leucine/Isoleucine`] must be modified to the RefMet Standarized name: "Leucine" (Error RN2)

##       (-) `refmet_name` [`Oxoglutaric acid`] must be modified to the RefMet Standarized name: "2-Oxoglutaric acid" (Error RN2)

##       (-) `refmet_name` [`Citric acid/Isocitric acid`] must be modified to the RefMet Standarized name: "Citric acid" (Error RN2)

##       (-) Total number of missed ids on MW: 3

##    - (-) SUMMARY: 3 `refmet_name` not found in RefMet Metabolomics Data Dictionary: FAIL

##   + (+) {rt} all numeric: OK

##   + (+) {mz} all numeric: OK

##   + (+) {`neutral_mass`} all numeric values OK

##   + (+) {formula} available: OK

check_metadata_samples(df = metadata_sample_named, cas = "umichigan")

##    - (-) `metadata_sample`: recently required COLUMN NAMES are missed: Adding with NA values: FAIL

##   + (+) All required columns present

##   + (+) `sample_id` seems OK

##   + (+) `sample_type` seems OK

##   + (+) `sample_order` is numeric

##   + (+) `sample_order` unique values OK

##   + (+) `raw_file` unique values: OK

##    - (-) `extraction_date` has NA values: FAIL

##    - (-) `acquisition_date` has NA values: FAIL

##    - (-) NA values detected in column ` lc_column_id `: FAIL

##    - ( ) Number of unique values in column ` lc_column_id `:  1

check_results(r_m = results_named, m_s = metadata_sample_named, m_m = metadata_metabolites_named)

##   + (+) All samples from `results_metabolite` are available in `metadata_sample`

##   + (+) `metabolite_name` is identical in both [results] and `metadata_metabolites` files: OK

##   + (+) `sample_id` columns are numeric: OK

How to process a metabolomics dataset

Two approaches available:

validate_metabolomics(input_results_folder = "/full/path/to/PROCESSED_YYYYMMDD", 
                      cas = "your_site_code")

validate_metabolomics(input_results_folder = "/full/path/to/PROCESSED_YYYYMMDD", 
                      cas = "your_site_code",
                      f_proof = TRUE,
                      out_qc_folder = "/path/to/the/folder/to/save/plots/",
                      printPDF = TRUE)

# Open the metadata_metabolites file(s)

metadata_metabolites_named <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)
metadata_metabolites_unnamed <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)

check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named")
check_metadata_metabolites(df = metadata_metabolites_unnamed, name_id = "unnamed")

# Open your files
metadata_sample_named <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)
metadata_sample_unnamed <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)

check_metadata_samples(df = metadata_sample_named, cas = "your_side_id")
check_metadata_samples(df = metadata_sample_unnamed, cas = "your_side_id")

# Open your files
metadata_metabolites_named <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)
metadata_sample_named <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)
results_named <- read.delim(file = "/path/to/your/file", stringsAsFactors = FALSE)

check_results(r_m = results_named, 
              m_s = metadata_sample_named, 
              m_m = metadata_metabolites_named)

Help

Additional details for each function can be found by typing, for example:

?validate_metabolomics

Need extra help? Please, either contact the BIC at motrpac-helpdesk@lists.stanford.edu and/or submit an issue here providing as many details as possible