getSegments

Return table of non-overlapping segments from GTFAnnotation object

Syntax

segments = getSegments(AnnotObj)

[segments,transcriptIDs] = getSegments(AnnotObj)

[___] = getSegments(AnnotObj,"Reference",R)

[___] = getSegments(AnnotObj"Gene",G)

[___] = getSegments(AnnotObj,"Transcript",T)

Description

segments = getSegments(AnnotObj) returns segments, a table of non-overlapping segments of nucleotide sequences built by flattening the transcripts in AnnotObj. If an exon boundary is not the same in two or more transcripts of a gene, then the function creates two or more non-overlapping segments which cover all exons in the transcript.

[segments,transcriptIDs] = getSegments(AnnotObj) returns transcriptIDs, a cell array of character vectors containing all unique transcript IDs in AnnotObj.

[___] = getSegments(AnnotObj,"Reference",R) returns the segments that belong to one or more references specified by R.

[___] = getSegments(AnnotObj"Gene",G) returns the segments that belong to one of more genes specified by G.

[___] = getSegments(AnnotObj,"Transcript",T) returns the segments that belong to one or more transcripts specified by T.

Examples

Retrieve Segments from a GTF-formatted File

Create a GTFAnnotation object from a GTF-formatted file.

obj = GTFAnnotation('hum37_2_1M.gtf');

Retrieve unique reference names. In this case, there is only one reference sequence, which is chromosome 2 (chr2).

ref = getReferenceNames(obj)

ref = 1x1 cell array
    {'chr2'}

Get a table of all non-overlapping segments of nucleotide sequences which belong to chr2.

segments = getSegments(obj,"Reference",ref);

Input Arguments

AnnotObj — GTF annotation

GTFAnnotation object

GTF annotation, specified as a GTFAnnotation object.

R — Names of reference sequences

character vector | string | string vector | cell array of character vectors | categorical array

Names of reference sequences, specified as a character vector, string, string vector, cell array of character vectors, or categorical array.

The names must come from the Reference field of AnnotObj. If a name does not exist, the function provides a warning and ignores it.

Data Types: char | string | cell | categorical

G — Names of genes

character vector | string | string vector | cell array of character vectors | categorical array

Names of genes, specified as a character vector, string, string vector, cell array of character vectors, or categorical array.

The names must come from the Gene field of AnnotObj. If a name does not exist, the function provides a warning and ignores the name.

Data Types: char | string | cell | categorical

T — Names of transcripts

character vector | string | string vector | cell array of character vectors | categorical array

Names of transcripts, specified as a character vector, string, string vector, cell array of character vectors, or categorical array.

The names must come from the Transcript field of AnnotObj. If a name does not exist, the function gives a warning and ignores the name.

Data Types: char | string | cell | categorical

Output Arguments

segments — Non-overlapping segments

table

Non-overlapping segments, returned as a table. The table contains the following variables for each segments.

Variable Name	Description
Start	Start location of each segment.
Stop	Stop location of each segment.
Reference	Categorical array representing the names of reference sequences to which the segments belong, obtained from the Reference field of AnnotObj.
ExonIndicator	Logical sparse matrix of segment versus exon. The rows represent segments. The columns are exons. If the ith segment is part of the jth exon, the element at position (i,j) is 1. Otherwise, it is 0.
TranscriptIndicator	Logical sparse matrix of segment versus transcript. The rows represent segments and the columns are transcripts. The element at position (i,j) is 1 if the ith segment is part of the jth transcript, and 0 otherwise.

transcriptIDs — Unique transcript IDs

cell array of character vectors

Unique transcript IDs, returned as a cell array of character vectors. The transcript IDs correspond to columns of the TranscriptIndicator variable of segments. For instance, the first element of transcriptIDs is the ID of the first column of TranscriptIndicator matrix.

Version History

Introduced in R2014b