Title:	Creation, Reading and Validation of 'mzqc' Files
Version:	0.7.0
Date:	2025-07-14
Description:	Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See https://hupo-psi.github.io/mzQC/ for details.
Imports:	jsonlite, jsonvalidate, knitr, methods, ontologyIndex, rmarkdown, R6, R6P, testthat, tools
VignetteBuilder:	knitr
License:	MIT + file LICENSE
URL:	https://github.com/MS-Quality-hub/rmzqc
BugReports:	https://github.com/MS-Quality-hub/rmzqc/issues
Encoding:	UTF-8
Config/testthat/edition:	3
RoxygenNote:	7.3.2
NeedsCompilation:	no
Packaged:	2025-07-15 19:17:48 UTC; bielow
Author:	Chris Bielow [aut, cre], David Jimenez-Morales [rev, ctb], Jeremi Maciejewski [ctb]
Maintainer:	Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Repository:	CRAN
Date/Publication:	2025-07-16 06:30:02 UTC

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

Description

Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See https://hupo-psi.github.io/mzQC/ for details.

Author(s)

Maintainer: Chris Bielow chris.bielow@bsc.fu-berlin.de (ORCID)

Other contributors:

• David Jimenez-Morales biodavidjm@gmail.com (ORCID) [reviewer, contributor]

• Jeremi Maciejewski jeremi.maciejewski5002@gmail.com [contributor]

See Also

Useful links:

• https://github.com/MS-Quality-hub/rmzqc

• Report bugs at https://github.com/MS-Quality-hub/rmzqc/issues

CV_

Description

Define a Singleton class which can hold a CV dictionary (so we do not have to load the .obo files over and over again)

Details

Get the full data by calling the 'getData()' function (which returns a list containing a 'CV', 'URI' and 'version'), or 'getCV()' which is a shorthand for 'getData()$CV'. You can set your own custom CV by calling 'setData()'. By default, the latest release of the PSI-MS-CV (see getCVDictionary). Wherever you need this data, simply re-grab the singleton using 'CV_$new()' (or use the convenience function getCVSingleton() from outside the package)

Super class

R6P::Singleton -> CV_

Methods

Public methods

• CV_$ensureHasData()

• CV_$byID()

• CV_$setData()

• CV_$getData()

• CV_$getCV()

Method ensureHasData()

Make sure that the CV data is loaded

Usage

CV_$ensureHasData()

Method byID()

A function to retrieve a CV entry using its ID

Usage

CV_$byID(id)

Arguments

Returns

A CV term, or NULL if the ID is unknown

Method setData()

Set a user-defined object (= a list of 'CV', 'URI' and 'version'), as obtained from getCVDictionary

Usage

CV_$setData(cv_data)

Arguments

Method getData()

Gets the underlying data (CV, URI and version)

Usage

CV_$getData()

Method getCV()

A shorthand for 'getData()$CV', i.e. the CV data.frame.

Usage

CV_$getCV()

Examples

## Not run: 
  cv_dict = CV_$new() ## uses 'getCVDictionary()' to populate the singleton
  cv_2 = CV_$new() ## uses the same data without parsing again
  cv_2$setData(getCVDictionary("custom", "https://my.com/custom.obo"))

## End(Not run)

An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.

Description

An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.

An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.

Details

The format is "%Y-%m-%dT%H:%M:%S".

Public fields

Methods

Public methods

• MzQCDateTime$new()

• MzQCDateTime$set()

• MzQCDateTime$isValid()

• MzQCDateTime$toJSON()

• MzQCDateTime$fromData()

• MzQCDateTime$clone()

Method new()

Constructor

Usage

MzQCDateTime$new(date = as.character(Sys.time()))

Arguments

Method set()

Sets datetime value

Usage

MzQCDateTime$set(date)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCDateTime$isValid(context = "MzQCDateTime")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCDateTime$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCDateTime$fromData(data, context = "MzQCDateTime")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCDateTime$clone(deep = FALSE)

Arguments

Examples

   dt1 = MzQCDateTime$new("1900-01-01")  ## yields "1900-01-01T00:00:00Z"
   dt2 = MzQCDateTime$new(Sys.time())
   ## test faulty input
   ## errors with 'character string is not in a standard unambiguous format'
   try(MzQCDateTime$new('lala'), silent=TRUE)
   ## test roundtrip conversion from/to JSON
   dt2$fromData(jsonlite::fromJSON(jsonlite::toJSON(dt1)))

Details of the software used to create the QC metrics

Description

Details of the software used to create the QC metrics

Details of the software used to create the QC metrics

Public fields

Methods

Public methods

• MzQCanalysisSoftware$new()

• MzQCanalysisSoftware$isValid()

• MzQCanalysisSoftware$toJSON()

• MzQCanalysisSoftware$fromData()

• MzQCanalysisSoftware$clone()

Method new()

Constructor

Usage

MzQCanalysisSoftware$new(
  accession = NA_character_,
  name = NA_character_,
  version = NA_character_,
  uri = NA_character_,
  description = NA_character_,
  value = NA_character_
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCanalysisSoftware$isValid(context = "MzQCanalysisSoftware")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCanalysisSoftware$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCanalysisSoftware$fromData(data, context = "MzQCanalysisSoftware")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCanalysisSoftware$clone(deep = FALSE)

Arguments

Base class of runQuality/setQuality

Description

Base class of runQuality/setQuality

Base class of runQuality/setQuality

Public fields

Methods

Public methods

• MzQCbaseQuality$new()

• MzQCbaseQuality$isValid()

• MzQCbaseQuality$getMetric()

• MzQCbaseQuality$toJSON()

• MzQCbaseQuality$fromData()

• MzQCbaseQuality$clone()

Method new()

Constructor

Usage

MzQCbaseQuality$new(metadata = MzQCmetadata$new(), qualityMetrics = list())

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCbaseQuality$isValid(context = "MzQCbaseQuality")

Arguments

Method getMetric()

Fetches metrics which match specified accession or name from the object.

Usage

MzQCbaseQuality$getMetric(accession = NULL, name = NULL)

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCbaseQuality$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCbaseQuality$fromData(mdata, context = "MzQCbaseQuality")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCbaseQuality$clone(deep = FALSE)

Arguments

Extract a certain metric from a runQuality's list of MzQCqualityMetric

Description

You must provide either the accession or the name of the metric, but not both.

Arguments

Details

Usually there should be only one MzQCqualityMetric which matches, however, this function will return all matches.

Note: this function will stop() if not results are found

Value

A list of MzQCqualityMetric's which match.

A controlled vocabulary document, usually pointing to an .obo file

Description

A controlled vocabulary document, usually pointing to an .obo file

A controlled vocabulary document, usually pointing to an .obo file

Public fields

Methods

Public methods

• MzQCcontrolledVocabulary$new()

• MzQCcontrolledVocabulary$isValid()

• MzQCcontrolledVocabulary$toJSON()

• MzQCcontrolledVocabulary$fromData()

• MzQCcontrolledVocabulary$clone()

Method new()

Constructor

Usage

MzQCcontrolledVocabulary$new(
  name = NA_character_,
  uri = NA_character_,
  version = NA_character_
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCcontrolledVocabulary$isValid(context = "MzQCcontrolledVocabulary")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCcontrolledVocabulary$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCcontrolledVocabulary$fromData(data, context = "MzQCcontrolledVocabulary")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCcontrolledVocabulary$clone(deep = FALSE)

Arguments

Examples

  MzQCcontrolledVocabulary$new(
    "Proteomics Standards Initiative Quality Control Ontology",
    "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.129/psi-ms.obo",
    "4.1.129")

A controlled vocabulary parameter, as detailed in the OBO file

Description

A controlled vocabulary parameter, as detailed in the OBO file

A controlled vocabulary parameter, as detailed in the OBO file

Public fields

Methods

Public methods

• MzQCcvParameter$new()

• MzQCcvParameter$isValid()

• MzQCcvParameter$toJSON()

• MzQCcvParameter$fromData()

• MzQCcvParameter$clone()

Method new()

Constructor

Usage

MzQCcvParameter$new(
  accession = NA_character_,
  name = NA_character_,
  value = NA,
  description = NA_character_
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCcvParameter$isValid(context = "MzQCcvParameter")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCcvParameter$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCcvParameter$fromData(data, context = "MzQCcvParameter")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCcvParameter$clone(deep = FALSE)

Arguments

Examples

  MzQCcvParameter$new("MS:4000070",
                      "retention time acquisition range",
                      c(0.2959, 5969.8172))
  isValidMzQC(MzQCcvParameter$new("MS:0000000"))

An inputfile within metadata for a run/setQuality

Description

An inputfile within metadata for a run/setQuality

An inputfile within metadata for a run/setQuality

Public fields

Methods

Public methods

• MzQCinputFile$new()

• MzQCinputFile$isValid()

• MzQCinputFile$toJSON()

• MzQCinputFile$fromData()

• MzQCinputFile$clone()

Method new()

Constructor

Usage

MzQCinputFile$new(
  name = NA_character_,
  location = NA_character_,
  fileFormat = MzQCcvParameter$new(),
  fileProperties = list()
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCinputFile$isValid(context = "MzQCinputFile")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCinputFile$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCinputFile$fromData(data, context = "MzQCinputFile")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCinputFile$clone(deep = FALSE)

Arguments

The metadata for a run/setQuality

Description

The metadata for a run/setQuality

The metadata for a run/setQuality

Public fields

Methods

Public methods

• MzQCmetadata$new()

• MzQCmetadata$isValid()

• MzQCmetadata$toJSON()

• MzQCmetadata$fromData()

• MzQCmetadata$clone()

Method new()

Constructor

Usage

MzQCmetadata$new(
  label = NA_character_,
  inputFiles = list(),
  analysisSoftware = list(),
  cvParameters = list()
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCmetadata$isValid(context = "MzQCmetadata")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCmetadata$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCmetadata$fromData(data, context = "MzQCmetadata")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCmetadata$clone(deep = FALSE)

Arguments

Root element of an mzQC document

Description

Root element of an mzQC document

Root element of an mzQC document

Details

At least one of runQualities or setQualities MUST be present.

Public fields

Methods

Public methods

• MzQCmzQC$new()

• MzQCmzQC$isValid()

• MzQCmzQC$toJSON()

• MzQCmzQC$fromData()

• MzQCmzQC$clone()

Method new()

Constructor

Usage

MzQCmzQC$new(
  version = NA_character_,
  creationDate = MzQCDateTime$new(),
  contactName = NA_character_,
  contactAddress = NA_character_,
  description = NA_character_,
  runQualities = list(),
  setQualities = list(),
  controlledVocabularies = list()
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCmzQC$isValid(context = "MzQCmzQC")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCmzQC$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCmzQC$fromData(data, context = "MzQCmzQC")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCmzQC$clone(deep = FALSE)

Arguments

The central class to store QC information

Description

The central class to store QC information

The central class to store QC information

Public fields

Methods

Public methods

• MzQCqualityMetric$new()

• MzQCqualityMetric$isValid()

• MzQCqualityMetric$toJSON()

• MzQCqualityMetric$fromData()

• MzQCqualityMetric$clone()

Method new()

Constructor

Usage

MzQCqualityMetric$new(
  accession = NA_character_,
  name = NA_character_,
  description = NA_character_,
  value = NA,
  unit = list()
)

Arguments

Method isValid()

Verifies validity of the object

Usage

MzQCqualityMetric$isValid(context = "MzQCqualityMetric")

Arguments

Method toJSON()

Creates JSON file from this object.

Usage

MzQCqualityMetric$toJSON(...)

Arguments

Method fromData()

Sets data for this object from plain named lists of R objects

Usage

MzQCqualityMetric$fromData(data, context = "MzQCqualityMetric")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCqualityMetric$clone(deep = FALSE)

Arguments

A runQuality object. Use to report metrics for individual runs which are independent of other runs.

Description

The object is an alias for MzQCbaseQuality.

Super class

rmzqc::MzQCbaseQuality -> MzQCrunQuality

Methods

Public methods

• MzQCrunQuality$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCrunQuality$clone(deep = FALSE)

Arguments

A setQuality object. Use it for metrics which are specific to sets, i.e. only for values which only make sense in the set context and cannot be stored as runQuality (see mzQC spec doc).

Description

The object is an alias for MzQCbaseQuality.

Super class

rmzqc::MzQCbaseQuality -> MzQCsetQuality

Methods

Public methods

• MzQCsetQuality$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

MzQCsetQuality$clone(deep = FALSE)

Arguments

Converts a NULL to NA; or returns the argument unchanged otherwise

Description

This is useful for missing list elements (which returns NULL), but when the missing element in refClass should be NA (and NULL would return an error)

Usage

NULL_to_NA(var_or_NULL)

Arguments

Examples

  NULL_to_NA(NA)   ## NA
  NULL_to_NA(NULL) ## NA
  NULL_to_NA("hi") ## "hi"

Converts a NULL to NA_character_; or returns the argument unchanged otherwise

Description

This is useful for missing list elements (which returns NULL), but when the missing element in refClass should be NA_character_ (and NULL would return an error)

Usage

NULL_to_charNA(char_or_NULL)

Arguments

Examples

  NULL_to_charNA(NA)   ## NA
  NULL_to_charNA(NULL) ## NA_character_
  NULL_to_charNA("hi") ## "hi"

Check for unexpected fields in data and warn if any are found

Description

This function compares the fields in the data with a list of expected fields and warns if there are any unexpected fields.

Usage

checkUnexpectedFields(data, expected_fields, class_name, context = NULL)

Arguments

Value

Invisibly returns a character vector of unexpected field names

Check if a field exists in data and warn if it doesn't, then return the field value

Description

Check if a field exists in data and warn if it doesn't, then return the field value

Usage

check_field_exists(
  data,
  field_name,
  class_name,
  context = NULL,
  default_value = NA
)

Arguments

Value

The field value if it exists, otherwise the default_value

Checks the value's class type, which should match at least of the types given in any_expected_class_types.

Description

Checks the value's class type, which should match at least of the types given in any_expected_class_types.

Usage

check_type(value, any_expected_class_types, expected_length = 0)

Arguments

Examples

  check_type(1, "numeric", 1)   # TRUE
  check_type("1", "numeric", 1) # FALSE
  check_type(1, "numeric", 2)   # FALSE
  check_type("ABC", "character", 1)             # TRUE
  check_type("ABC", "character")                # TRUE
  check_type("ABC", "character", 2)             # FALSE
  check_type(c("ABC", "DEF"), "character", 2)   # TRUE
  check_type(1.1, c("numeric", "double"))    # TRUE
  check_type(1.1, c("numeric", "double"), 1) # TRUE
  check_type(matrix(1:9, nrow=3), "matrix")   # TRUE
  check_type(data.frame(a=1:3, b=4:6), c("something", "data.frame"))   # TRUE

For a given filename (e.g. "test.mzML"), check the suffix and translate it to an PSI-MS CV term, e.g. 'MS:1000584'

Description

The following mapping is currently known: .raw : MS:1000563 ! Thermo RAW format .mzML : MS:1000584 ! mzML format .mzData : MS:1000564 ! PSI mzData format .wiff : MS:1000562 ! ABI WIFF format .pkl : MS:1000565 ! Micromass PKL format .mzXML : MS:1000566 ! ISB mzXML format .yep : MS:1000567 ! Bruker/Agilent YEP format .dta : MS:1000613 ! Sequest DTA format .mzMLb : MS:1002838 ! mzMLb format

Usage

filenameToCV(filepath)

Arguments

Details

Falls back to 'MS:1000560 ! mass spectrometer file format' if no match could be found.

Upper/lowercase is ignored, i.e. "mzML == mzml".

Value

A CV term accession as string, e.g. 'MS:1000584'

Examples

  filenameToCV("test.mZmL")  # MS:1000584
  filenameToCV("test.raw")  # MS:1000563
  filenameToCV(c("test.raw", "bla.mzML"))

Allow conversion of plain named lists of R objects (from jSON) to mzQC objects

Description

Allow conversion of plain named lists of R objects (from jSON) to mzQC objects

Usage

fromDatatoMzQC(mzqc_class, data, context = NULL)

Arguments

Examples

    data = rmzqc::MzQCcvParameter$new("acc", "myName", "value")
    data_recovered = rmzqc::fromDatatoMzQC(rmzqc::MzQCcvParameter,
                         list(jsonlite::fromJSON(jsonlite::toJSON(data))))

Allow conversion of a plain R object (obtained from jSON) to an mzQC object

Description

If you have a list of elements, call fromDatatoMzQC.

Usage

fromDatatoMzQCobj(mzqc_class, data, context = NULL)

Arguments

Examples

 data = MzQCcvParameter$new("acc", "myName", "value")
 data_recovered = fromDatatoMzQCobj(MzQCcvParameter, jsonlite::fromJSON(jsonlite::toJSON(data)))
 data_recovered

Fetch and parse the 'psi-ms.obo' and some metadata from the usual sources to use as ontology.

Description

If use_local_fallback is TRUE, this function will never fail. Otherwise, it may fail if the internet connection is flawed or internal URLs related to GitHubs API become stale.

Usage

getCVDictionary(
  source = c("latest", "local", "custom"),
  custom_uri = NULL,
  use_local_fallback = TRUE
)

Arguments

Details

A 'pato.obo', and 'uo.obo' from the 'rmzqc/cv/' folder are automatically merged into the result.

See CV_ class to use this function efficiently.

Value

A list with 'CV', 'URI' and 'version', where 'CV' is a data.frame with columns 'id', 'name', 'def', 'parents', 'children' (and many more) which contains the CV entries

Returns an MzQCcontrolledVocabulary for the currently used CV (see getCVSingleton) using getCVSingleton()$getData()$URI and ⁠$version⁠.

Description

Returns an MzQCcontrolledVocabulary for the currently used CV (see getCVSingleton) using getCVSingleton()$getData()$URI and ⁠$version⁠.

Usage

getCVInfo()

Returns the CV singleton. See CV_.

Description

Returns the CV singleton. See CV_.

Usage

getCVSingleton()

Fills a MzQCcvParameter object with id(accession) and name. The value (if any) needs to be set afterwards.

Description

Fills a MzQCcvParameter object with id(accession) and name. The value (if any) needs to be set afterwards.

Usage

getCVTemplate(accession, CV = getCVSingleton())

Arguments

Value

An instance of MzQCcvParameter

Returns an MzQCcontrolledVocabulary for the currently used CV (see getCVSingleton)

Description

Returns an MzQCcontrolledVocabulary for the currently used CV (see getCVSingleton)

Usage

getDefaultCV()

Note

This function will be deprecated soon. Use getCVInfo instead.

Get the latest PSI-MS CV release URL

Description

This may fail (e.g. if no internet connection is available, or URLs became invalid) then 'NULL' will be returned instead of an URL. A warning may be emitted, if the URL is out of date (i.e. the GitHub API changed).

Usage

getLatest_PSICV_URL()

Obtains the 'data-version' from a local (i.e. non-url) PSI-MS-CV

Description

Obtains the 'data-version' from a local (i.e. non-url) PSI-MS-CV

Usage

getLocal_CV_Version(local_PSIMS_obo_file)

Arguments

Examples

 getLocal_CV_Version(system.file("./cv/psi-ms.obo", package="rmzqc")) # "4.1.95"

Get an optional value from data, using a default if not present

Description

Use this function for optional fields where no warning should be generated if missing.

Usage

getOptionalValue(data, field_name, default_value = NA)

Arguments

Value

The field value if it exists, otherwise the default_value

Fills a MzQCqualityMetric object with id(accession) and name. The value (if any) and unit (if any) need to be set afterwards.

Description

The accession must be valid (or allow_unknown_id must be TRUE)

Usage

getQualityMetricTemplate(
  accession,
  CV = getCVSingleton(),
  allow_unknown_id = FALSE
)

Arguments

Value

An instance of MzQCqualityMetric

Get a syntax validator for mzQC

Description

Get a syntax validator for mzQC

Usage

getSyntaxValidator()

Checks if filepath ends in suffix (ignoring lower/upper case differences). If suffix does not start with a '.' it is prepended automatically.

Description

Checks if filepath ends in suffix (ignoring lower/upper case differences). If suffix does not start with a '.' it is prepended automatically.

Usage

hasFileSuffix(filepath, suffix)

Arguments

Value

TRUE if yes, FALSE otherwise

Examples

  hasFileSuffix("bla.txt", "txt")    # TRUE
  hasFileSuffix("bla.txt", ".txt")   # TRUE
  hasFileSuffix("bla.txt", ".TXT")   # TRUE
  hasFileSuffix("foo", "")           # TRUE
  hasFileSuffix("", "")              # TRUE
  hasFileSuffix("bla.txt", "doc")    # FALSE
  hasFileSuffix("bla.txt", ".doc")   # FALSE
  hasFileSuffix("fo", ".doc")        # FALSE
  hasFileSuffix("", ".doc")          # FALSE

Tell if a variable's value is undefined (NA or NULL); If yes, and it is required by the mzQC standard, we can raise an error.

Description

You can pass multiple variable, which are all checked. If any of them is undefined, the function returns TRUE

Usage

isUndefined(s, ..., verbose = TRUE, context = NULL)

Arguments

Examples

isUndefined(NA)       ## TRUE
isUndefined(NULL)     ## TRUE
isUndefined(NA, NULL) ## TRUE
isUndefined("")       ## FALSE
isUndefined(list(1,2,3)) ## FALSE
isUndefined("", NA)   ## TRUE
isUndefined(NA, "")   ## TRUE
isUndefined(1)        ## FALSE
myVar = NA
isUndefined(myVar)    ## TRUE, with warning "Variable 'myVar' is NA/NULL!"

Checks validity (= completeness) of mzQC objects - or lists (JSON arrays) thereof

Description

Note: Returns TRUE for empty lists!

Usage

isValidMzQC(x, parent_context = NULL)

Arguments

Details

This function checks if an mzQC object or a list of mzQC objects is valid. For lists, all elements need to be valid for the function to return TRUE. The function provides detailed error messages that include the path to the invalid field, making it easier to identify validation issues in complex nested structures.

Examples

  isValidMzQC(MzQCcvParameter$new("MS:4000059"))       # FALSE
  isValidMzQC(MzQCcvParameter$new("MS:4000059", "Number of MS1 spectra")) # TRUE
  isValidMzQC(list(MzQCcvParameter$new("MS:4000059"))) # FALSE
  isValidMzQC(list(MzQCcvParameter$new("MS:4000059", "Number of MS1 spectra"))) # TRUE

Convert a local filename, e.g. "./myData/test.mzML" to a proper URI (e.g. "file:///user/bielow/myData/test.mzML")

Description

Relative filenames are made absolute. Backslashes as path separators are replaced by forward slashes (as commonly seen on Windows).

Usage

localFileToURI(local_filename, must_exist = TRUE)

Arguments

Value

A URI starting with "file:///" followed by an absolute path

Get the information of each CV term from an obo file.

Description

Get the information of each CV term from an obo file.

Usage

parseOBO(cv_obo_file)

Arguments

Value

A data.frame containing CV term information

Read a JSON file in mzQC format into an MzQCmzQC root object

Description

Read a JSON file in mzQC format into an MzQCmzQC root object

Usage

readMZQC(filepath)

Arguments

Value

An MzQCmzQC root object from which all the data can be extracted/manipulated

Read a JSON object in mzQC format into an MzQCmzQC root object

Description

Read a JSON object in mzQC format into an MzQCmzQC root object

Usage

readMZQCFromJSON(json_obj)

Arguments

Value

An MzQCmzQC root object from which all the data can be extracted/manipulated

Removes the last suffix (including the last dot) from a filename. If no dot exists, the full string is returned.

Description

Removes the last suffix (including the last dot) from a filename. If no dot exists, the full string is returned.

Usage

removeFileSuffix(filepath)

Arguments

Value

The input with removed suffix

Examples

 removeFileSuffix("test.tar.gz")  # --> 'test.tar'
 removeFileSuffix("test.mzML")  # --> 'test'
 removeFileSuffix("/path/to/test.mzML")  # --> '/path/to/test'
 removeFileSuffix("test_no_dot")  # --> 'test_no_dot'

Remove a file, if it exists (useful for temporary files which may or may not have been created)

Description

Remove a file, if it exists (useful for temporary files which may or may not have been created)

Usage

removeIfExists(tmp_filename)

Arguments

Value

NULL if file is missing, otherwise TRUE/FALSE depening on successful removal

From an ID, e.g. "MS:1003162" (for PTX-QC), and some additional information, create an 'analysisSoftware' node for mzQC

Description

From an ID, e.g. "MS:1003162" (for PTX-QC), and some additional information, create an 'analysisSoftware' node for mzQC

Usage

toAnalysisSoftware(id, version = "unknown", uri = NULL, value = NA_character_)

Arguments

Value

An MzQCanalysisSoftware object

Examples

 # use 'version = packageVersion("PTXQC")' if the package is installed
 toAnalysisSoftware(id = "MS:1003162", version = "1.0.12")

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

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 (MS:4000006): 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")
   

Syntactically validates an mzQC document which is present as a file.

Description

The returned TRUE/FALSE has additional attributes in case of errors. Use attributes(result) to access them.

Usage

validateFromFile(filepath, verbose = TRUE)

Arguments

Value

TRUE/FALSE if validation was successful/failed

Syntactically validates an mzQC document which is already in memory as mzQC root object, as obtained by, e.g. readMZQC().

Description

This method is less performant than validateFromString, because it needs to convert the R object to a JSON string first.

Usage

validateFromObj(mzqc_root, verbose = TRUE)

Arguments

Details

The returned TRUE/FALSE has additional attributes in case of errors. Use attributes(result) to access them.

Value

TRUE/FALSE if validation was successful/failed

Syntactically validates an mzQC document which is already in memory as JSON string. e.g. the string "{ mzQC : {}}"

Description

If the string object passed into this function contains multiple elements (length > 1). then they will be concatenated using '\n' before validation.

Usage

validateFromString(JSON_string, verbose = TRUE)

Arguments

Details

The returned TRUE/FALSE has additional attributes in case of errors. Use attributes(result) to access them.

Value

TRUE/FALSE if validation was successful/failed

Writes a full mzQC object to disk.

Description

You can in theory also provide any mzQC subelement, but the resulting mzQC file will not validate since its incomplete.

Usage

writeMZQC(filepath, mzqc_obj)

Arguments

Details

The filename should have '.mzQC' (case sensitive) as suffix. There will be a warning otherwise.