GTFAnnotation class

Represent Gene Transfer Format (GTF) annotations

Description

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

You construct a GTFAnnotation object from
a GTF-formatted file. 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.

Construction

Annotobj =
GTFAnnotation(File)
constructs Annotobj,
a GTFAnnotation object, from File,
a GTF-formatted file.

Input Arguments

File

Character vector specifying a GTF-formatted file.

Properties

FieldNames

Cell array of character vectors specifying the names of the
available data fields for each annotation in the GTFAnnotation object.
This property is read only.

NumEntries

Integer specifying number of annotations in the GTFAnnotation object.
This property is read only.

Methods

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

Copy Semantics

Value. To learn how value classes affect
copy operations, see Copying Objects in
the MATLAB® documentation.

Indexing

GTFAnnotation objects support dot . indexing
to extract properties.

Examples

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: {1x11 cell}
    NumEntries: 308

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