mzIDCollection-class: A class to handle a set of mzID objects

In mzID: An mzIdentML parser for R

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

mzID documentation built on Nov. 8, 2020, 8:08 p.m.