getRange

Retrieve range of annotations from GTFAnnotation or GFFAnnotation object

Syntax

Range = getRange(AnnotObj)

Description

Range = getRange(AnnotObj) returns Range, a 1-by-2 numeric array specifying the minimum and maximum positions in the reference sequence covered by annotations in AnnotObj.

Examples

Retrieve Range of Annotations from a GTFAnnotation Object

Construct a GTFAnnotation object from a GTF-formatted file that is provided with Bioinformatics Toolbox™, and then return the range of the feature annotations.

Construct a GTFAnnotation object from a GTF file.

GTFAnnotObj = GTFAnnotation('hum37_2_1M.gtf');

Return first and last positions of reference associated with feature annotations.

range = getRange(GTFAnnotObj)

range = 1x2 int32 row vector

     41609   1371382

Retrieve Range of Annotations from a GFFAnnotation Object

Construct a GFFAnnotation object from a GFF-formatted file that is provided with Bioinformatics Toolbox™, and then return the range of the feature annotations.

Construct a GFFAnnotation object from a GFF file.

GFFAnnotObj = GFFAnnotation('tair8_1.gff');

Return first and last positions of reference associated with feature annotations.

range = getRange(GFFAnnotObj)

range = 1x2 int32 row vector

     3631   498516

Input Arguments

AnnotObj — Feature annotations

GTFAnnotation object | GFFAnnotation object

Feature annotations, specified as a GTFAnnotation or GFFAnnotation object.

Output Arguments

Range — Minimum and maximum positions in the reference sequence covered by annotations in AnnotObj

1-by-2 numeric array

Minimum and maximum positions in the reference sequence covered by annotations in AnnotObj, returned as a 1-by-2 numeric array.

Tips

• Use the getSubset method with the Reference name-value pair to return a GFFAnnotation object containing only one reference sequence. Then use this subsetted object as input to the getRange function.

Version History

Introduced in R2011b