Create an 'MzQCqualityMetric' object from two inputs

toQCMetric(id, value, on_violation = c("error", "warn"))

Arguments

id: The CV accession
value: The data, as computed by some QC software in the required format.
on_violation: What to do when 'value' is not of the correct type (according to the given 'id')? Default: "error"; or "warn"

Value

An MzQCanalysisSoftware object

Details

The inputs are:

an ID of a QC metric, e.g. "MS:4000059" (number of MS1 spectra)
a value

The value must be in the correct format depending on the metric. The value type (see below) is checked (a warning/error is given if mismatching): The following requirements for values apply:

single value: R single value; the unit is obtained from the CVs 'has_units'
n-tuple: an R vector, e.g. using c(1,2,3), i.e. all values have the same type; the unit is obtained from the CVs 'has_units'
table: an R data.frame(); all columns defined using CVs 'has_column' must be present (a warning/error is given otherwise)
matrix: an R matrix, i.e. all values have the same type; the unit is obtained from the CVs 'has_units'

Upon violation, an error (default) or a warning is emitted:


   toQCMetric(id = "MS:4000059", value = data.frame(n = 1)) # errors: wrong value format

Examples

   toQCMetric(id = "MS:4000059", value = 13405) # number of MS1 spectra
#> Reference class object of class "MzQCqualityMetric"
#> Field "accession":
#> [1] "MS:4000059"
#> Field "name":
#> [1] "number of MS1 spectra"
#> Field "description":
#> [1] "\"The number of MS1 events in the run.\" [PSI:MS]"
#> Field "value":
#> [1] 13405
#> Field "unit":
#> list()