NMF: atrack – R documentation

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atrack

Annotation Tracks

Description

.atrack is an S4 generic method that converts an object into an annotation track object. It provides a general and flexible annotation framework that is used by aheatmap to annotates heatmap rows and columns.

is.atrack tests if an object is an annotationTrack object.

adata get/sets the annotation parameters on an object

amargin get/sets the annotation margin, i.e. along which dimension of the data the annotations are to be considered.

anames returns the reference margin names for annotation tracks, from their embedded annotation data object.

alength returns the reference length for annotation tracks, from their embedded annotation data object

atrack creates/concatenates annotationTrack objects

annotationTrack is constructor function for annotationTrack object

Usage

.atrack(object, ...)

  is.atrack(x)

  adata(x, value, ...)

  amargin(x, value)

  anames(x, default.margin)

  alength(x, default.margin)

  ## S4 method for signature 'ANY'
.atrack(object, data = NULL, ...)

  atrack(..., order = NULL, enforceNames = FALSE,
    .SPECIAL = NA, .DATA = NULL, .CACHE = NULL)

  annotationTrack(x = list())

Arguments

`object`	an object from which is extracted annotation tracks
`...`	extra arguments to allow extensions and passed to the next method call. For `atrack`, arguments in `...` are concatenated into a single `annotationTrack` object.
`x`	an R object
`value`	replacement value for the complete annotation data list
`default.margin`	margin to use if no margin data is stored in the `x`.
`data`	object used to extend the annotation track within a given data context. It is typically a matrix-like object, against which annotation specifications are matched using `match_atrack`.
`order`	an integer vector that indicates the order of the annotation tracks in the result list
`enforceNames`	logical that indicates if missing track names should be generated as `X<i>`
`.SPECIAL`	an optional list of functions (with no arguments) that are called to generate special annotation tracks defined by codes of the form `':NAME'`. e.g., the function `link{consensusmap}` defines special tracks `':basis'` and `':consensus'`. If `.SPECIAL=FALSE`, then any special tracks is discarded and a warning is thrown.
`.DATA`	data used to match and extend annotation specifications. It is passed to argument `data` of the `.atrack` methods, which in turn use pass it to `match_atrack`.
`.CACHE`	an `annotationTrack` object with which the generated annotation track should be consistent. This argument is more for internal/advanced usage and should not be used by the end-user.

Details

Methods for .atrack exist for common type of objects, which should provide enough options for new methods to define how annotation track are extracted from more complex objects, by coercing/filtering them into a supported type.

Value

atrack returns a list, decorated with class 'annotationTrack', where each element contains the description of an annotation track.

Methods

.atrack: signature(object = "ANY"): The default method converts character or integer vectors into factors. Numeric vectors, factors, a single NA or annotationTrack objects are returned unchanged (except from reordering by argument order). Data frames are not changed either, but class 'annotationTrack' is appended to their original class set.

NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

v0.23.0

GPL (>= 2)

Authors

Renaud Gaujoux, Cathal Seoighe

Initial release

2020-07-30