Superclasses:
Contain General Feature Format (GFF) annotations
The GFFAnnotation class contains annotations for one or more reference
sequences, conforming to the GFF file format.
You construct a GFFAnnotation object from
a GFF- or 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.
Annotobj =
GFFAnnotation(File)Annotobj,
a GFFAnnotation object, from File,
a GFF- or GTF-formatted file.
|
Character vector or string specifying a GFF- or GTF-formatted file. |
|
Cell array of Character vectors specifying the names of the
available data fields for each annotation in the |
|
Integer specifying number of annotations in the |
| getData | Create structure containing subset of data from
GFFAnnotation |
| getFeatureNames | Retrieve unique feature names from GFFAnnotation object |
| getIndex | Return index array of annotations from GFFAnnotation object |
| getRange | Retrieve range of annotations from GFFAnnotation object |
| getReferenceNames | Retrieve reference names from GFFAnnotation object |
| getSubset | Retrieve subset of elements from GFFAnnotation object |
Value. To learn how value classes affect copy operations, see Copying Objects.
GFFAnnotation objects support dot . indexing
to extract properties.
Construct a GFFAnnotation object
from a GFF-formatted file that is provided with Bioinformatics Toolbox™:
GFFAnnotObj = GFFAnnotation('tair8_1.gff')GFFAnnotObj =
GFFAnnotation with properties:
FieldNames: {'Reference' 'Start' 'Stop' 'Feature' 'Source' 'Score' 'Strand' 'Frame' 'Attributes'}
NumEntries: 3331Construct a GFFAnnotation object from a GTF-formatted file that is
provided with Bioinformatics Toolbox:
GFFAnnotObj = GFFAnnotation('hum37_2_1M.gtf')GFFAnnotObj =
GFFAnnotation with properties:
FieldNames: {'Reference' 'Start' 'Stop' 'Feature' 'Source' 'Score' 'Strand' 'Frame' 'Attributes'}
NumEntries: 308