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setReference

Specify reference sequence for Genomics Viewer

Since R2024a

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Syntax

setReference(gv,referenceFile)
setReference(gv,referenceFile,Cytoband=cytobandFile)

Description

setReference(gv,referenceFile) specifies referenceFile, a file containing the reference sequence for use in the Genomics Viewer app specified by the genomicsViewer object gv.

example

setReference(gv,referenceFile,Cytoband=cytobandFile) also specifies the corresponding cytoband ideogram file for the reference chromosomes.

Examples

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Open Live Script

This example requires an internet connection.

Open the Genomics Viewer app. By default, the app uses the human genome (GRCh38/hg38) as the reference sequence.

gv = genomicsViewer;

Change the reference sequence to the mouse genome (GRCm39/mm39) and specify the corresponding cytoband file.

setReference(gv,"https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa",...
                Cytoband="https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/cytoBandIdeo.txt.gz");

In the IGV panel, click Chromosome 1 to zoom in on it.

For more information on other interactive visualization options, see Visualize NGS Data Using Genomics Viewer App.

Close the app.

close(gv);

Input Arguments

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Genomics viewer object, specified as a genomicsViewer object.

Name of a reference sequence file, specified as a character vector or string scalar. Specify a local FASTA-formatted file or a URL to a remote file. If you specify a URL, it must start with http, https, or gs. Other file transfer protocols, such as FTP, are not supported.

Data Types: char | string

Name of a cytoband ideogram file for reference chromosomes, specified as a character vector or string scalar. Specify a local file or a URL to a remote file. If you specify a URL, it must start with http, https, or gs. Other file transfer protocols, such as FTP, are not supported. For more information on cytoband files, see cytobandread and chromosomeplot.

Data Types: char | string | cell

Version History

Introduced in R2024a

See Also

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