GTFAnnotation

Contain Gene Transfer Format (GTF) annotations

Description

The GTFAnnotation object contains annotations for one or more reference sequences, conforming to the GTF file format.

Each element in the object represents an annotation. Use the object properties and methods to filter annotations by feature, reference sequence, or reference sequence position. Use object methods to extract data for a subset of annotations into an array of structures.

Creation

Construct a GTFAnnotation object from a GTF-formatted file.

Annotobj = GTFAnnotation(File) constructs a GTFAnnotation object Annotobj from File. Here, File is a character vector or string specifying a GTF-formatted file.

Properties

FieldNames — Names of the available data fields for each annotation in the GTFAnnotation object

cell array of character vectors

Names of the available data fields for each annotation in the GTFAnnotation object, returned as a cell array of character vectors. This property is read only.

Data Types: cell

NumEntries — Number of annotations in the GTFAnnotation object

integer

Number of annotations in the GTFAnnotation object, returned as an integer. This property is read only.

Data Types: double

Object Functions

getData	Create structure containing subset of data from GTFAnnotation or GFFAnnotation object
getExons	Return table of exons from GTFAnnotation object
getFeatureNames	Retrieve unique feature names from GTFAnnotation or GFFAnnotation object
getGeneNames	Retrieve unique gene names from GTFAnnotation object
getGenes	Return table of unique genes in GTFAnnotation object
getIndex	Return index array of annotations from GTFAnnotation or GFFAnnotation object
getRange	Retrieve range of annotations from GTFAnnotation or GFFAnnotation object
getReferenceNames	Retrieve reference names from GTFAnnotation or GFFAnnotation object
getSegments	Return table of non-overlapping segments from GTFAnnotation object
getSubset	Retrieve subset of elements from GTFAnnotation or GFFAnnotation object
getTranscriptNames	Retrieve unique transcript names from GTFAnnotation object
getTranscripts	Return table of unique transcripts in GTFAnnotation object

Examples

Create GTFAnnotation Object

Construct a GTFAnnotation object from a GTF-formatted file that is provided with Bioinformatics Toolbox™.

GTFAnnotObj = GTFAnnotation('hum37_2_1M.gtf')

GTFAnnotObj = 
  GTFAnnotation with properties:

    FieldNames: {'Reference'  'Start'  'Stop'  'Feature'  'Gene'  'Transcript'  'Source'  'Score'  'Strand'  'Frame'  'Attributes'}
    NumEntries: 308

Version History

Introduced in R2011b