Package 'rmzqc' reference manual

Title:	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.
Authors:	Chris Bielow [aut, cre] , David Jimenez-Morales [rev, ctb]
Maintainer:	Chris Bielow <[email protected]>
License:	MIT + file LICENSE
Version:	0.5.4
Built:	2024-11-12 03:40:38 UTC
Source:	https://github.com/ms-quality-hub/rmzqc

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)
check_type(value, any_expected_class_types, expected_length = 0)

Arguments

`value`	A certain value (e.g. a single value, data.frame etc)
`any_expected_class_types`	A vector of valid class types, any of which the @p value should have
`expected_length`	The expected length of value (usually to check if its a single value); 0 (default) indicates that length can be ignored

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

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

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

Inherited methods

R6P::Singleton$initialize()

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

id: A CV accession, e.g. 'MS:1000560'

Method `setData()`

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

Usage

CV_$setData(cv_data)

Arguments

cv_data: The result of a call to getCVDictionary

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()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

CV_$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

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)

## 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)

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)
filenameToCV(filepath)

Arguments

filepath

A filename (with optional path)

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"))

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)
fromDatatoMzQC(mzqc_class, data)

Arguments

`mzqc_class`	Prototype of the class to convert 'data' into
`data`	A list of: A datastructure of R lists/arrays as obtained by 'jsonlite::fromJSON()'

Examples

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

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)
fromDatatoMzQCobj(mzqc_class, data)

Arguments

`mzqc_class`	Prototype of the class to convert 'data' into
`data`	A datastructure of R lists/arrays as obtained by 'jsonlite::fromJSON()'

Examples

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

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

Arguments

`source`	Where to get the PSI-MS CV from: - 'latest' will download 'psi-ms.obo' from https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest - 'local' will use rmzqc/cv/psi-ms.obo' (which might be outdated, if you need the latest terms) - 'custom' uses a user-defined URI in 'custom_uri'
`custom_uri`	Used when 'source' is set to 'custom'. The URI can be local or remote, e.g. 'c:/obo/my.obo' or 'https://www.abc.com/my.obo'
`use_local_fallback`	When downloading a file from a URI fails, should we fall back to the local psi-ms.obo shipped with rmzqc?

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()
getCVInfo()

Returns the CV singleton. See `CV_`.

Description

Returns the CV singleton. See CV_.

Usage

getCVSingleton()
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())
getCVTemplate(accession, CV = getCVSingleton())

Arguments

`accession`	The ID (=accession) of the term in the CV
`CV`	A CV dictionary, as obtained by getCVDictionary(); defaults to the global singleton, which is populated automatically

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()
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()
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)
getLocal_CV_Version(local_PSIMS_obo_file)

Arguments

local_PSIMS_obo_file

A path to a local file, e.g. 'c:/temp/my.obo'

Examples

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

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

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

Description

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

Usage

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

Arguments

`accession`	The ID (=accession) of the term in the CV
`CV`	A CV dictionary, as obtained by getCVDictionary(); defaults to the global singleton, which is populated automatically

Value

An instance of MzQCqualityMetric

Get a syntax validator for mzQC

Description

Get a syntax validator for mzQC

Usage

getSyntaxValidator()
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)
hasFileSuffix(filepath, suffix)

Arguments

`filepath`	A relative or absolute path to a file, whose suffix is checked
`suffix`	This is the suffix we expect (the '.' is prepended internally if missing)

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

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 string is undefined (NA or NULL); If yes, and its required by the mzQC standard, we can raise an error.

Description

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

Usage

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

Arguments

`s`	A string to be checked for NA/NULL
`...`	More strings to be checked
`verbose`	If TRUE and 's' is NULL/NA, will print the name of the variable which was passed in

Examples

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

isUndefined(NA)       ## TRUE
isUndefined(NULL)     ## TRUE
isUndefined(NA, NULL) ## TRUE
isUndefined("")       ## 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, ...)
isValidMzQC(x, ...)

Arguments

`x`	An mzQC refclass (or list of them), each will be subjected to `isValidMzQC()`
`...`	Ellipsis, for recursive argument splitting

Details

You can pass multiple arguments, which are all checked individually. All of them need to be valid, for TRUE to be returned. The reason for combining both list support for arguments and ellipsis (...) into this function is that JSON arrays are represented as lists and you can simply pass them as a single argument (without the need for do.call()) and get the indices of invalid objects (if any). The ellipsis is useful to avoid clutter, i.e. if (!isValidMzQC(a) || !isValidMzQC(b)) doStuff() is harder to read than if (!isValidMzQC(a,b)) doStuff()

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

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

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)
localFileToURI(local_filename, must_exist = TRUE)

Arguments

`local_filename`	Path to a file (can be relative to current getwd(); or absolute)
`must_exist`	Require the file to exist

Value

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

Details of the software used to create the QC metrics

Description

Details of the software used to create the QC metrics

Fields

accession: Accession number identifying the term within its controlled vocabulary.
name: Name of the controlled vocabulary term describing the software tool.
version: Version number of the software tool.
uri: Publicly accessible URI of the software tool or documentation.
description: (optional) Definition of the controlled vocabulary term.
value: (optional) Name of the software tool.

Base class of runQuality/setQuality

Description

Base class of runQuality/setQuality

Fields

metadata: The metadata for this run/setQuality
qualityMetrics: Array of MzQCqualityMetric objects

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

Description

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

Fields

name: Full name of the controlled vocabulary.
uri: Publicly accessible URI of the controlled vocabulary.
version: (optional) Version of the controlled vocabulary.

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")

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

Fields

accession: Accession number identifying the term within its controlled vocabulary.
name: Name of the controlled vocabulary term describing the parameter.
value: (optional) Value of the parameter.
description: (optional) Definition of the controlled vocabulary term.

Examples

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

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

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

Description

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

Fields

datetime: A correctly formatted date time (use as read-only)

Examples

   dt1 = MzQCDateTime$new("1900-01-01")  ## yields "1900-01-01T00:00:00"
   dt2 = MzQCDateTime$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)))

dt1 = MzQCDateTime$new("1900-01-01")  ## yields "1900-01-01T00:00:00"
   dt2 = MzQCDateTime$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)))

An inputfile within metadata for a run/setQuality

Description

An inputfile within metadata for a run/setQuality

Fields

name: The name MUST uniquely match to a location (specified below) listed in the mzQC file.
location: Unique file location, REQUIRED to be specified as a URI. The file URI is RECOMMENDED to be publicly accessible.
fileFormat: An MzQCcvParameter with 'accession' and 'name'.
fileProperties: An array of MzQCcvParameter, usually with 'accession', 'name' and 'value'. Recommended are at least two entries: a) Completion time of the input file (MS:1000747) and b) Checksum of the input file (any child of: MS:1000561 ! data file checksum type).

The metadata for a run/setQuality

Description

The metadata for a run/setQuality

Fields

label: Unique name for the run (for runQuality) or set (for setQuality).
inputFiles: Array/list of MzQCinputFile objects
analysisSoftware: Array/list of MzQCanalysisSoftware objects
cvParameters: (optional) Array of cvParameters objects

Root element of an mzQC document

Description

At least one of runQualities or setQualities MUST be present.

Fields

version: Version of the mzQC format.
creationDate: Creation date of the mzQC file.
contactName: Name of the operator/creator of this mzQC file.
contactAddress: Contact address (mail/e-mail or phone)
description: Description and comments about the mzQC file contents.
runQualities: Array of MzQCrunQuality;
setQualities: Array of MzQCsetQuality
controlledVocabularies: Array of CV domains used (obo files)

The central class to store QC information

Description

The central class to store QC information

Fields

accession: Accession number identifying the term within its controlled vocabulary.
name: Name of the controlled vocabulary element describing the metric.
description: (optional) Definition of the controlled vocabulary term.
value: (optional) Value of the metric (single value, n-tuple, table, matrix). The structure is not checked by our mzQC implementation and must be handled by the caller, see toQCMetric.
unit: (optional) Array of unit(s), stored as MzQcvParameter

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

Description

The object is an alias for MzQCbaseQuality.

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.

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)
NULL_to_charNA(char_or_NULL)

Arguments

char_or_NULL

A string or NULL

Examples

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

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

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)
NULL_to_NA(var_or_NULL)

Arguments

var_or_NULL

A variable of any kind or NULL

Examples

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

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

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)
parseOBO(cv_obo_file)

Arguments

cv_obo_file

A local path to an .obo file

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)
readMZQC(filepath)

Arguments

filepath

A filename (with path) to read from.

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)
removeFileSuffix(filepath)

Arguments

filepath

A filename (with optional path – which is retained)

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'

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)
removeIfExists(tmp_filename)

Arguments

tmp_filename

A path to a local file

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

Arguments

`id`	The CV accession
`version`	The version of the tool which created the metric/mzQC
`uri`	URI to the homepage, or if NULL (default), will be extracted from the definition in the PSI MS-CV (if possible)
`value`	An optional name for the software (if different from the CV's name)

Value

An MzQCanalysisSoftware object

Examples

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

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

Create an 'MzQCqualityMetric' object from two inputs

Description

Create an 'MzQCqualityMetric' object from two inputs

Usage

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

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

Value

An MzQCanalysisSoftware object

Examples

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

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

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)
validateFromFile(filepath, verbose = TRUE)

Arguments

`filepath`	A path to a file (e.g. "c:/my.mzQC", or "test.mzQC")
`verbose`	Show extra information if validation fails

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)
validateFromObj(mzqc_root, verbose = TRUE)

Arguments

`mzqc_root`	An mzQC root object
`verbose`	Show extra information if validation fails

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)
validateFromString(JSON_string, verbose = TRUE)

Arguments

`JSON_string`	A string which contains JSON (multiple lines allowed)
`verbose`	Show extra information if validation fails

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)
writeMZQC(filepath, mzqc_obj)

Arguments

`filepath`	A filename (with optional path) to write to.
`mzqc_obj`	An MzQCmzQC root object, which is serialized to JSON and then written to disk

Details

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

Package 'rmzqc'

Help Index

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

Description

Usage

Arguments

Examples

CV_

Description

Details

Super class

Methods

Public methods

Method ensureHasData()

Usage

Method byID()

Usage

Arguments

Method setData()

Usage

Arguments

Method getData()

Usage

Method getCV()

Usage

Method clone()

Usage

Arguments

Examples

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

Usage

Arguments

Details

Value

Examples

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

Description

Usage

Arguments

Examples

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

Description

Usage

Arguments

Examples

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

Description

Usage

Arguments

Details

Value

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

Description

Usage

Returns the CV singleton. See CV_.

Description

Usage

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

Description

Usage

Arguments

Value

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

Description

Usage

Note

Get the latest PSI-MS CV release URL

Description

Usage

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

Description

Usage

Arguments

Examples

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

Description

Usage

Arguments

Value

Method `ensureHasData()`

Method `byID()`

Method `setData()`

Method `getData()`

Method `getCV()`

Method `clone()`

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

Returns the CV singleton. See `CV_`.

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