GenomicAnnotations-class {PREDA} | R Documentation

## Class "GenomicAnnotations" to manage information about genomic features

### Description

This class is used to manage information about genomic features under investigation: i.e. genomic genes, SNP or others, with particular focus on the genomic coordinates of each of them. Other additional annotations associated to each element can be stored in a GenomicAnnotations object in the optionalAnnotations slots

### Objects from the Class

Objects can be created by calls of the form `new("GenomicAnnotations", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders)`.

### Slots

`ids`:

  Object of class `"character"` ~~

`chr`:

  Object of class `"integer"` ~~

`start`:

  Object of class `"integer"` ~~

`end`:

  Object of class `"integer"` ~~

`strand`:

  Object of class `"numeric"` ~~

`chromosomesNumbers`:

  Object of class `"numeric"` ~~

`chromosomesLabels`:

  Object of class `"character"` ~~

`optionalAnnotations`:

  Object of class `"matrix"` ~~

`optionalAnnotationsHeaders`:

  Object of class `"character"` ~~

### Methods

GenomicAnnotations2dataframe

  `signature(.Object = "GenomicAnnotations")`: extracts annotations as a dataframe with probeids as rownames

GenomicAnnotations2GenomicAnnotationsForPREDA

  `signature(.Object = "GenomicAnnotations")`: generate a new GenomicAnnotationsForPREDA object from a GenomicAnnotations object

GenomicAnnotations2reference_positions

  `signature(.Object = "GenomicAnnotations")`: extract from the GenomicAnnotations object a vector containing a vector with reference positions

GenomicAnnotationsExtract

  `signature(.Object = "GenomicAnnotations")`: extract optional annotations for a specific region

GenomicAnnotationsFilter_neg

  `signature(.Object = "GenomicAnnotations")`: filter annotations to remove selected chromosomes

GenomicAnnotationsFilter_pos

  `signature(.Object = "GenomicAnnotations")`: filter annotations to keep selected chromosomes

GenomicAnnotationsSortAndCleanNA

  `signature(.Object = "GenomicAnnotations")`: sort annotations according to selected chromosomes and to remove genes containing any NA annotation field

GenomicRegionsAnnotate

  `signature(.Object1 = "GenomicRegions", .Object2 = "GenomicAnnotations")`: extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object

initialize

  `signature(.Object = "GenomicAnnotations")`: initialize method for GenomicAnnotations objects

### Note

This class is better described in the package vignette

### Author(s)

Francesco Ferrari

### See Also

`GenomicAnnotations2dataframe`, `GenomicAnnotations2GenomicAnnotationsForPREDA`, `GenomicAnnotations2reference_positions`,`GenomicAnnotationsExtract`, `GenomicAnnotationsFilter_neg`,`GenomicAnnotationsFilter_pos`, `GenomicAnnotationsSortAndCleanNA`,`GenomicRegionsAnnotate`,

### Examples

    showClass("GenomicAnnotations")

[Package PREDA version 1.40.0 Index]