This short guide provides a quick overview of the core functions to
use the mwbenchr package to interact with mass spectrometry
and study data. For a complete tutorial, refer to the Getting
Started section of the documentation.
First, load the mwbenchr package:
Create a client to interact with the API:
client <- mw_rest_client()Fetch compound information by providing its PubChem CID. Here, we use
CID 5281365 as an example:
compound <- get_compound_by_pubchem_cid(client, 5281365)
print(compound)
#> # A tibble: 1 × 12
#> pubchem_cid regno formula exactmass inchi_key name sys_name lm_id kegg_id
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 5281365 28467 C20H34O 290.260966 OJISWRZIEWC… Gera… 3,7,11,… LMPR… C09094
#> # ℹ 3 more variables: chebi_id <chr>, metacyc_id <chr>, smiles <chr>Retrieve data from a study by providing its study ID (e.g.,
"ST000001"). Convert the response into a data frame:
study_data <- get_study_data(client, "ST000001")
study_df <- response_to_df(study_data)
head(study_df)
#> # A tibble: 6 × 8
#> study_id analysis_id analysis_summary metabolite_name metabolite_id
#> <chr> <chr> <chr> <chr> <chr>
#> 1 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> 2 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> 3 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> 4 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> 5 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> 6 ST000001 AN000001 GCMS positive ion mode 1,2,4-benzenetriol ME000097
#> # ℹ 3 more variables: refmet_name <chr>, units <chr>, DATA <named list>If you want to search for compounds based on their mass (optional):
Search for studies related to Diabetes in Human blood samples. The result is returned as a data frame:
diabetes_studies <- search_metstat(
client,
species = "Human",
sample_source = "Blood",
disease = "Diabetes"
)Convert the result to a data frame and view:
diabetes_df <- response_to_df(diabetes_studies)
head(diabetes_df)
#> # A tibble: 6 × 6
#> row_id study study_title species source disease
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Row1 ST003897 Postprandial Plasma Lipidomic Changes … Human Blood Diabet…
#> 2 Row2 ST003896 Postprandial Plasma Metabolomic Change… Human Blood Diabet…
#> 3 Row3 ST003895 Postprandial Plasma Metabolomic Change… Human Blood Diabet…
#> 4 Row4 ST003894 Postprandial Plasma Lipidomic Changes … Human Blood Diabet…
#> 5 Row5 ST003671 Discovery of Metabolic Biomarkers for … Human Blood Diabet…
#> 6 Row6 ST003636 Individual glycemic responses to carbo… Human Blood Diabet…Session Info
sessioninfo::session_info()
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#>
#> ──────────────────────────────────────────────────────────────────────────────Here, we covered just fundamental implemented methods in the
mwbenchr package, including how to interact with compound
and study data, as well as how to search for mass spectrometry-related
compounds and studies.
For more detailed examples and additional functions, please refer to the Getting Started of the package, which covers the full tutorial.