check metadata samples

Source: R/metabolomics_qc.R

check whether metadata_sample is following guidelines

check_metadata_samples(
  df,
  cas,
  assay = "OTHER",
  return_n_issues = FALSE,
  verbose = TRUE
)

Arguments

df

(data.frame) metadata_metabolites

cas

(char) CAS site code

assay

(char) Assay code. Options:

  • CONV: for Duke's conventional metabolites

  • OTHER (default): all the other assays.

return_n_issues

(logical) if TRUE returns the number of issues.

verbose

(logical) TRUE (default) shows messages

Value

(int) number of issues identified

Examples

{
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