Package 'mzID'

A parser for the mzIdentML file format

Description

Using the mzID function this package is able to parse mzIdentML files into an mzID class instance. Multiple files can be parsed in parallel into an mzIDCollection which is a list-like class that handles multiple mzID objects.

Details

The key functionalities are described in the following pages:

• mzID:Parse mzIdentML files

• mzID-class:Class to store the data from an mzIdentML file

• mzIDCollection-class:Class to store multiple mzID objects

• mzID-getters:Access the data stored in mzID and mzIDCollection objects

• flatten:Converts the content of an mzID object to a table with respect to the peptide-spectrum matches

The package is maintained at its GitHub repository where feature requests and bugs can be directed. Questions and bugs can furthermore be posted at the Bioconductor support site

Author(s)

Thomas Lin Pedersen with contributions from Laurent Gatto

---

Flatten an mzID related class into a table

Description

This function flattens the content of the object into a table by merging the content intelligently (it knows the links between the different objects).

Usage

flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDpsm'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDpeptides'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzID'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
flatten(object, safeNames = TRUE)

Arguments

object	The object to be flattened
safeNames	Logical. Should column names be lowered to ensure compitability between different versions of the mzIdentML schema. Defaults to TRUE

Value

A data.frame with the flattened result or a list of data.frames

Methods (by class)

• mzIDpsm: Merge id and scans according to the mapping

• mzIDpeptides: Merge peptides with their modifications

• mzID: Flatten an mzID object with respect to psm'

• mzIDCollection: Flatten all mzID object in the collection into a list of data frames.

See Also

mzID-class mzIDCollection-class mzIDpsm mzIDpeptides

Examples

exampleFile <- system.file('extdata', '55merge_tandem.mzid', package = 'mzID')
mzResults <- mzID(exampleFile)
head(flatten(mzResults))

---

Parse an mzIdentML file

Description

This function takes a single mzIdentML file and parses it into an mzID object.

Usage

mzID(file, verbose = TRUE)

Arguments

file	A character string giving the location of the mzIdentML file to be parsed
verbose	Logical Should information be printed to the console? Default is TRUE

Details

The mzID function uses the XML package to read the content of an mzIdentML file and store it in an mzID object. Unlike how mzR handles mzML files, mzID parses everything in one chunk. Memory can thus be a problem for very big datasets, but as mzIdentML files are not indexed, it is ineficient to access the data dynamically.

If multiple filenames are passed to the function they will be processed in parallel using foreach and doParallel. The number of workers spawned is either the maximal number of available cores or the number of files to parse, whichever is smallest. The return value will in these cases be an mzIDCollection object. If some of the files cannot be parsed they will not be contained in the returned object and a warning will be issued. No errors will be thrown.

Value

An mzID object

See Also

mzID-class mzIDCollection-class

Examples

# Parsing of the example files provided by HUPO:
exampleFiles <- list.files(system.file('extdata', package = 'mzID'), 
                           pattern = '*.mzid', full.names = TRUE)
mzID(exampleFiles[1])

mzID(exampleFiles[2])

mzID(exampleFiles[3])

mzID(exampleFiles[4])

mzID(exampleFiles[5])

mzID(exampleFiles[6])

mzID(exampleFiles[7])

mzID(exampleFiles[8])

mzID(exampleFiles[9])

# Parsing into an mzIDCollection
collection <- mzID(exampleFiles[1:3])
names(collection)

---

A class to contain data from mzIdentML-files

Description

This class stores all parsed information from mzIdentML files

Usage

## S4 method for signature 'mzID'
show(object)

## S4 method for signature 'mzID'
length(x)

## S4 method for signature 'mzID'
removeDecoy(object)

## S4 method for signature 'mzID'
database(object, safeNames = TRUE)

## S4 method for signature 'mzID'
evidence(object, safeNames = TRUE)

## S4 method for signature 'mzID'
parameters(object)

## S4 method for signature 'mzID'
software(object)

## S4 method for signature 'mzID'
files(object)

## S4 method for signature 'mzID'
peptides(object, safeNames = TRUE)

## S4 method for signature 'mzID'
modifications(object)

## S4 method for signature 'mzID'
id(object, safeNames = TRUE)

## S4 method for signature 'mzID'
scans(object, safeNames = TRUE)

## S4 method for signature 'mzID'
idScanMap(object)

## S4 method for signature 'mzID'
c(x, y, ..., recursive = FALSE)

Arguments

object	An mzID object
x	An mzID object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?
y	An mzID or mzIDCollection object
...	ignored
recursive	ignored

Details

The mzID class stores information in a subset of classes, each class having its own slot. While these classes should not need to be accessed directly, descriptions of their content is delegated to each respective class.

Methods (by generic)

• show: Short summary of object content

• length: Get number of psm' in object

• removeDecoy: Remove decoys from mzID object

• database: Get the database used for searching

• evidence: Get the evidence from the peptide search

• parameters: Get the parameters used for the search

• software: Get the software used to arrive at the results

• files: Get the data files used for the analysis

• peptides: Get the peptides identified.

• modifications: Get the modification on the identified peptides

• id: Get the identification results

• scans: Get the scans matched to peptides

• idScanMap: Get the link between scans and identifications

• c: Combine mzID and mzIDCollection objects

Slots

parameters

An instance of mzIDparameters-class. This object contains all information related to how the analysis was carried out.

psm

An instance of mzIDpsm-class. This object contains the meat of the analysis with all scans and their related PSMs recorded.

peptides

An instance of mzIDpeptides-class. This object contains a library of all peptides generated from the database along with possible modifications.

evidence

An instance of mzIDevidence-class. This object lists all peptides detected in the analysis with reference to the mzIDpeptides instance.

database

An instance of mzIDdatabase-class. This object contains information on the proteins in the database. As the full database is not recorded in mzIdentML files the actual protein sequence is not recorded but there is sufficient information to retrieve it from the database file.

Objects from the class

Objects can be created using the mzID constructor, which handles parsing of mzIdentML files

References

http://www.psidev.info/mzidentml

See Also

mzID

Other mzID.classes: mzIDCollection-class, mzIDdatabase-class, mzIDevidence-class, mzIDparameters-class, mzIDpeptides-class, mzIDpsm-class

---

Getter functions for identification data

Description

This set of functions are used to extract data from mzID and mzIDCollection objects.

Usage

evidence(object, safeNames = TRUE)

id(object, safeNames = TRUE)

idScanMap(object)

parameters(object)

software(object)

files(object)

Arguments

object	An mzID or mzIDCollection object
safeNames	Logical. Should column names be lowered to ensure compitability between different versions of the mzIdentML schema. Defaults to TRUE

Value

A data frame or a list of data frames in the case of mzIDCollections

See Also

mzID-class mzIDCollection-class

---

Create a new mzIDCollection

Description

This function creates a new mzIDCollection object containing the supplied mzID object. As such the result is equivalent to passing a number of mzID objects to c(), except that an empty mzIDCollection object is returned if no mzID objects are supplied.

Usage

mzIDCollection(...)

Arguments

...	An arbitrary number of mzID objects

Value

An mzIDCollection object

See Also

mzID-class mzIDCollection-class

---

A class to handle a set of mzID objects

Description

This class is a container for multiple mzID objects. It is constructed such that the bulk data are not copied when passed around. It is the aim that this class have parity with the mzID class in the methods it exposes to the user, such that mzIDCollections can be thought of as vectors in the traditional R sense. Furthermore it accepts standard indexing and concatenation.

Usage

## S4 method for signature 'mzIDCollection'
show(object)

## S4 method for signature 'mzIDCollection'
length(x)

as.list.mzIDCollection(object)

## S4 method for signature 'mzIDCollection'
removeDecoy(object)

## S4 method for signature 'mzIDCollection'
names(x)

## S4 replacement method for signature 'mzIDCollection,character'
names(x) <- value

## S4 method for signature 'mzIDCollection,numeric,missing'
x[[i, j, ...]]

## S4 method for signature 'mzIDCollection,character,missing'
x[[i, j, ...]]

## S4 method for signature 'mzIDCollection,numeric,missing,missing'
x[i, j, drop]

## S4 method for signature 'mzIDCollection,character,missing,missing'
x[i, j, drop]

## S4 method for signature 'mzIDCollection,logical,missing,missing'
x[i, j, drop]

## S4 method for signature 'mzIDCollection'
c(x, y, ..., recursive = FALSE)

## S4 method for signature 'mzIDCollection'
database(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
evidence(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
parameters(object)

## S4 method for signature 'mzIDCollection'
software(object)

## S4 method for signature 'mzIDCollection'
files(object)

## S4 method for signature 'mzIDCollection'
peptides(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
modifications(object)

## S4 method for signature 'mzIDCollection'
id(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
scans(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
idScanMap(object)

Arguments

object	An mzIDCollection object
x	An mzIDCollection object
value	A character vector of desired names
i	An integer or a string giving the index or the name respectively
j	ignored
...	ignored
drop	ignored
y	An mzID or mzIDCollection object
recursive	ignored
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

Objects of this class is usually constructed be passing mulitple files to the mzID constructor, or by combining mulitple mzID objects.

Methods (by generic)

• show: A short summary of the content of the object

• length: Return the number of mzID object in the collection

• removeDecoy: Removes decoys in all mzID object in collection

• names: Get the names of the mzID object stored in the collection

• names<-: Set the names of the mzID object stored in the collection

• [[: Extract an mzID object by index

• [[: Extract an mzID object by name

• [: Subset collection by index

• [: Subset collection by name

• [: Subset collection by logical value

• c: Combine mzIDCollction and mzID objects

• database: Get the database used for searching

• evidence: Get the evidence from the peptide search

• parameters: Get the parameters used for the search

• software: Get the software used to arrive at the results

• files: Get the data files used for the analysis

• peptides: Get the peptides identified.

• modifications: Get the modification on the identified peptides

• id: Get the identification results

• scans: Get the scans matched to peptides

• idScanMap: Get the link between scans and identifications

Slots

data

An environment that holds the individual mzID objects

.lookup

A matrix with indexing information for retriving the mzID objects in the @data slot.

See Also

mzID mzIDCollection

Other mzID.classes: mzID-class, mzIDdatabase-class, mzIDevidence-class, mzIDparameters-class, mzIDpeptides-class, mzIDpsm-class

---

A constructor for the mzIDdatabase class

Description

This function handles parsing of data and construction of an mzIDdatabase object. This function is not intended to be called explicitly but as part of an mzID construction. Thus, the function is not exported.

Usage

mzIDdatabase(doc, ns, addFinalizer = FALSE, path)

Arguments

doc	an XMLInternalDocument created using xmlInternalTreeParse
ns	The appropriate namespace for the doc, as a named character vector with the namespace named x
addFinalizer	Logical Sets whether reference counting should be turned on
path	If doc is missing the file specified here will be parsed

Value

An mzIDdatabase object

See Also

mzIDdatabase-class

---

A class to store database information from an mzIdentML file

Description

This class handles parsing and storage of database information from mzIDentML files, residing at the /MzIdentML/SequenceCollection/DBSequence node.

Usage

## S4 method for signature 'mzIDdatabase'
show(object)

## S4 method for signature 'mzIDdatabase'
length(x)

## S4 method for signature 'mzIDdatabase'
database(object, safeNames = TRUE)

Arguments

object	An mzIDevidence object
x	An mzIDdatabase object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The content of the class is stored in a data.frame with columns depending on the content of the mzIdentML file. Required information for files conforming to the mzIdentML standard are: 'accession', 'searchDatabase_ref' and 'id', while additional information can fx be 'length' (number of residues), 'description' (from the fasta file) and 'sequence' (the actual sequence).

Methods (by generic)

• show: Short summary of the content of the object

• length: Report the number of proteins in the database

• database: Get the database used for searching

Slots

database

A data.frame containing references to all the database sequences from the mzIdentML file

Objects from the class

Objects of mzIDdatabase are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDdatabase.

See Also

mzIDdatabase

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDevidence-class, mzIDparameters-class, mzIDpeptides-class, mzIDpsm-class

---

A constructor for the mzIDevidence class

Description

This function handles parsing of data and construction of an mzIDevidence object. This function is not intended to be called explicitly but as part of an mzID construction. Thus, the function is not exported.

Usage

mzIDevidence(doc, ns, addFinalizer = FALSE, path)

Arguments

doc	an XMLInternalDocument created using xmlInternalTreeParse
ns	The appropriate namespace for the doc, as a named character vector with the namespace named x
addFinalizer	Logical Sets whether reference counting should be turned on
path	If doc is missing the file specified here will be parsed

Value

An mzIDevidence object

See Also

mzIDevidence-class

---

A class to store peptide evidence information from an mzIdentML file

Description

This class handles parsing and storage of peptide evidence information from mzIDentML files, residing at the /*/x:SequenceCollection/x:PeptideEvidence node.

Usage

## S4 method for signature 'mzIDevidence'
show(object)

## S4 method for signature 'mzIDevidence'
length(x)

## S4 method for signature 'mzIDevidence'
evidence(object, safeNames = TRUE)

Arguments

object	An mzIDevidence object
x	An mzIDevidence object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The content of the class is stored in a data.frame with columns depending on the content of the mzIdentML file. Columns represent the attribute values of for each PeptideEvidence node. For files conforming to the HUPO standard, dbSequence_ref, id and peptide_ref is required while start, end, pre, post, name, isDecoy, frame and translationTable_ref are optional. Information residing in cvParam and userParam children are not parsed.

Methods (by generic)

• show: Short summary of the content of the object

• length: Report number of evidence

• evidence: Get the evidence from the peptide search

Slots

evidence

A data.frame containing all peptide evidence from the mzIdentML file

Objects from the class

Objects of mzIDevidence are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDevidence.

See Also

mzIDevidence

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDparameters-class, mzIDpeptides-class, mzIDpsm-class

---

A constructor for the mzIDparameters class

Description

This function handles parsing of data and construction of an mzIDparameters object. This function is not intended to be called explicitly but as part of an mzID construction. Thus, the function is not exported. It relies on a number of getter functions to retrive the different information from around the document.

Usage

mzIDparameters(doc, ns, addFinalizer = FALSE, path)

Arguments

doc	an XMLInternalDocument created using xmlInternalTreeParse
ns	The appropriate namespace for the doc, as a named character vector with the namespace named x
addFinalizer	Logical Sets whether reference counting should be turned on
path	If doc is missing the file specified here will be parsed

Value

An mzIDparameters object

See Also

mzIDparameters-class

---

A Class to store analysis information from the mzIdentML file

Description

This class tries to collect the multitude of different analysis information required to rerun the analysis. The intended data to be stored are: The software used in the analysis of the data, the location and nature of the rawfile(s), the location and nature of the database file(s), the location of the mzIDentML file itself as well as all the parameters used during the analysis leading to the mzIdentML file. Information regarding how the LC-MS experiment was performed should be collected from the raw data file. As the parameters used in different software solutions can vary greatly, all these parameters are stored in a named list, which can thus be very different from pipeline to pipeline. It is the users responsibility to check conformity between samples.

Usage

## S4 method for signature 'mzIDparameters'
show(object)

## S4 method for signature 'mzIDparameters'
length(x)

## S4 method for signature 'mzIDparameters'
parameters(object)

## S4 method for signature 'mzIDparameters'
software(object)

## S4 method for signature 'mzIDparameters'
files(object)

Arguments

object	An mzIDparameters object
x	An mzIDparameters object

Methods (by generic)

• show: Short summary of the content

• length: Get the length of the object

• parameters: Get the parameters used for the search

• software: Get the software used to arrive at the results

• files: Get the data files used for the analysis

Slots

software

A data frame with information retaining to the software used for the analysis. At least the name and an id is given, but optionally also version number and URI.

rawFile

A data frame with information about the raw data file(s) used for the analysis. The data frame will contain at least the location and spectrum ID format.

databaseFile

A data frame containing at least the location and file format of the database file used in the search.

idFile

A character string containing the location of the mzIdentML file at the time of parsing.

parameters

A list containing containing the information stored in the MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol node. SearchType and Threshold are the only required parameters given by the mzIdentML standard.

Objects from the class

Objects of mzIDparameters are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDparameters (not exported).

See Also

mzIDparameters

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDevidence-class, mzIDpeptides-class, mzIDpsm-class

---

A constructor for the mzIDpeptides class

Description

This function handles parsing of data and construction of an mzIDpeptides object. This function is not intended to be called explicitly but as part of an mzID construction. Thus, the function is not exported.

Usage

mzIDpeptides(doc, ns, addFinalizer = FALSE, path)

Arguments

doc	an XMLInternalDocument created using xmlInternalTreeParse
ns	The appropriate namespace for the doc, as a named character vector with the namespace named x
addFinalizer	Logical Sets whether reference counting should be turned on
path	If doc is missing the file specified here will be parsed

Value

An mzIDpeptides object

See Also

mzIDpeptides-class

---

A class to store peptide information from an mzIdentML file

Description

This class handles parsing and storage of peptide information from mzIDentML files, residing at the /x:MzIdentML/x:SequenceCollection/x:Peptide node.

Usage

## S4 method for signature 'mzIDpeptides'
show(object)

## S4 method for signature 'mzIDpeptides'
length(x)

## S4 method for signature 'mzIDpeptides'
peptides(object, safeNames = TRUE)

## S4 method for signature 'mzIDpeptides'
modifications(object)

Arguments

object	An mzIDpeptides object
x	An mzIDpeptides object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The information is stored in a dataframe with an id, an optinal name and the amino acid sequence of the peptide. Alongside a list is stored with modification information of each peptide. Each row in the dataframe has a corresponding entry en the list. If no modification of the peptide is present the entry is NULL, if a modification is present the entry is a dataframe, listing the different modifications of the peptide.

Methods (by generic)

• show: Short summary of the content of the object

• length: Report the number of peptides

• peptides: Get the peptides identified.

• modifications: Get the modification on the identified peptides

Slots

peptides

A data.frame containing all peptides used in the search

modifications

A list containing possible modifications of the peptides listed in @peptides

Objects from the class

Objects of mzIDpeptides are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDpeptides.

See Also

mzIDpeptides

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDevidence-class, mzIDparameters-class, mzIDpsm-class

---

A constructor for the mzIDpsm class

Description

This function handles parsing of data and construction of an mzIDpsm object. This function is not intended to be called explicitly but as part of an mzID construction. Thus, the function is not exported.

Usage

mzIDpsm(doc, ns, addFinalizer = FALSE, path)

Arguments

doc	an XMLInternalDocument created using xmlInternalTreeParse
ns	The appropriate namespace for the doc, as a named character vector with the namespace named x.
addFinalizer	Logical Sets whether reference counting should be turned on.
path	If doc is missing the file specified here will be parsed.

Value

An mzIDpsm object

See Also

mzIDpsm-class

---

A class to store psm information from an mzIdentML file

Description

This class handles parsing and storage of scan info and the related psm's. This information resides in the /*/x:DataCollection/x:AnalysisData/x:SpectrumIdentificationList/x:SpectrumIdentificationResult node.

Usage

## S4 method for signature 'mzIDpsm'
show(object)

## S4 method for signature 'mzIDpsm'
length(x)

## S4 method for signature 'mzIDpsm'
id(object, safeNames = TRUE)

## S4 method for signature 'mzIDpsm'
scans(object, safeNames = TRUE)

## S4 method for signature 'mzIDpsm'
idScanMap(object)

Arguments

object	An mzIDpsm object
x	An mzIDpsm object
safeNames	Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The content of the class is stored as two data frames: One containing a row for each scan in the results, and one containing all psm's in the results. Additionally a list containing indexing from scan to psm is stored.

Methods (by generic)

• show: A short summary of the content

• length: Get the number of psm'

• id: Get the identification results

• scans: Get the scans matched to peptides

• idScanMap: Get the link between scans and identifications

Slots

scans

A data.frame containing all reference to all scans with at least one psm. The columns gives at least an ID, a spectrumID and a reference to the file used.

id

A data.frame containing all psm's from the analysis. The columns depend on the file but at least id, chargeState, experimentalMassToCharge, passThreshold and rank must exist according to the mzIdentML specifications.

mapping

A list with an entry for each row in @scans. Each entry contains an integer vector pointing to the related rows in @id.

Objects from the class

Objects of mzIDpsm are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDpsm.

See Also

mzIDpsm

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDevidence-class, mzIDparameters-class, mzIDpeptides-class

---

Remove decoy identification

Description

This function trims down an mzID or mzIDCollection object by removing all information that is only related to the decoy database search. If some information relates to both the regular and decoy database (e.g. a peptide sequence that can be found in both databases) it is kept.

Usage

removeDecoy(object, ...)

Arguments

object	An mzID or mzIDCollection to remove decoy information from
...	Currently ignored

Value

An mzID or mzIDCollection object depending on the input

See Also

mzID-class mzIDCollection-class

---