annotation-utils: Handling Object Annotations

In renozao/xbioc: Extra Base Functions for Bioconductor

Description

Annotation utility functions.

Usage

hasAnnotation(object, ...)

getAnnotation(object, ...)

## Default S3 method:
getAnnotation(object, ..., null = TRUE)

setAnnotation(object, value, ...)

## Default S3 method:
setAnnotation(object, value, as.attribute = TRUE, ...)

## S3 method for class 'list'
getAnnotation(object, ...)

## S3 method for class 'list'
setAnnotation(object, value, force = FALSE, ...)

Arguments

object	an object
...	extra parameters (currently not used)
null	logical that indicates if an empty character string should be return as NULL.
value	new annotation string, e.g., 'hgu133plu2.db'.
as.attribute	logical that indicates that the annotation string can be stored as an attribute, if no suitable `annotation <-` method is found.
force	single logical that indicates if the annotation string should be set even if the objects do not share the same original annotation.

Functions

• hasAnnotation: tells if an object has some – non empty – attached annotation.

• getAnnotation: try extracting embedded annotations.

• getAnnotation.default: the default method returns NULL if the object contains no annotation.

• setAnnotation: embbeds an annotation string into an object (typically the name of an annotation package, e.g., 'hgu133plus2.db').

  setAnnotation uses a suitable annotation<- method if it exists, or sets the annotation string into attribute 'annotation'. It returns the modified object.

• getAnnotation.list: gets annotation for each element in a list of ExpressionSet objects.

• setAnnotation.list: set annotation on each element of a list of ExpressionSet objects.

Methods (by generic)

getAnnotation:

• getAnnotation(default): the default method returns NULL if the object contains no annotation.

• getAnnotation(list): gets annotation for each element in a list of ExpressionSet objects.

setAnnotation:

• setAnnotation(list): set annotation on each element of a list of ExpressionSet objects.

renozao/xbioc documentation built on Sept. 3, 2020, 1:13 a.m.