toQCMetric: Create an 'MzQCqualityMetric' object from two inputs (id and...

In rmzqc: Creation, Reading and Validation of 'mzqc' Files

Create an 'MzQCqualityMetric' object from two inputs (id and value).

Description

Create an 'MzQCqualityMetric' object from two inputs (id and value).

Usage

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

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"
allow_unknown_id	Allows invalid accession, and also does not check the value type; if 'FALSE' this function errors

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 deduced 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 deduced from the CVs 'has_units'

• table: an R list(); 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 deduced from the CVs 'has_units'

Upon violation of the value type (e.g. data.frame instead of single value), an error or a warning is emitted (see @p on_violation):

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

Value

An MzQCanalysisSoftware object

Examples

   ## single value
   toQCMetric(id = "MS:4000059", value = 13405) # number of MS1 spectra

   ## n-tuple
   toQCMetric(id = "MS:4000051", value = c(31.3, 35.99, 38.44)) # XIC-FWHM quantiles

   ## table
   toQCMetric(id = "MS:4000063",  # MS2 known precursor charges fractions
              value = list("MS:1000041" = 1:3,
                           "UO:0000191" = c(0.7, 0.6, 0.8)))

   ## test an invalid CV accession/id
   toQCMetric(id = "MS:0000", value = "ID_is_not_valid", allow_unknown_id = TRUE)

   
   ## matrix (there is no example in the CV yet, so this cannot be tested)
   toQCMetric(id = "MS:400000?", value = matrix(1:12, nrow = 3, ncol = 4)) # ???
   # does not work since the 'id' is not derived from a valid value type
   toQCMetric(id = "MS:0000000", value = "ID_is_not_valid")

   # does not work, since the ID is unknown and 'allow_unknown_id' is FALSE by default
   toQCMetric(id = "MS:0000", value = "ID_is_not_valid")
   

rmzqc documentation built on April 4, 2025, 2:46 a.m.