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

Description Usage Arguments Details Methods (by generic) Slots See Also

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

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## 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)

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.