Skip to contents

check metadata metabolites

Source: R/metabolomics_qc.R
check_metadata_metabolites.Rd

check whether metadata_metabolites is following guidelines

Usage

check_metadata_metabolites(
  df,
  name_id,
  return_n_issues = FALSE,
  refmet_validation = TRUE,
  verbose = TRUE
)

Arguments

df

(data.frame) metadata_metabolites

name_id

(char) specify whether named or unnamed files

return_n_issues

(logical) if TRUE returns the number of issues.

refmet_validation

(logical) TRUE (default) validates every refmet_name against the Metabolomics Workbench API (one request per metabolite, slow). FALSE skips only the API calls: the refmet_name column-presence and uniqueness checks always run.

verbose

(logical) TRUE (default) shows messages

Value

(int) number of issues identified

Examples

{
check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named")
}
#>   + (+) All required columns present
#>   + (+) `metabolite_name` OK
#>   + (+) `refmet_name validation`: unique values: OK
#>   + (+) `refmet_name validation`: connecting to Metabolomics Workbench for validation (slow)
#>    - (-) `refmet_name validation`: [`Oxoglutaric acid`] must be modified to the RefMet Standardized name: "2-Oxoglutaric acid" (Error RN2)
#>    - (-) `refmet_name validation`: Total number of missed ids on MW: 1
#>    - (-) `refmet_name validation`: 1 `refmet_name` not found in RefMet: FAIL
#>   + (+) {rt} all numeric: OK
#>   + (+) {mz} all numeric: OK
#>   + (+) {`neutral_mass`} all numeric values OK
#>   + (+) {formula} available: OK