Table 2

Example of GRanges object

seqnames

ranges

strand

tx_id

exon_id


1

chrX

[48242968], [48243005]

+

35775

132624

2

chrX

[48243475], [48243563]

+

35775

132625

3

chrX

[48244003], [48244117]

+

35775

132626

4

chrX

[48244794], [48244889]

+

35775

132627

5

chrX

[48246753], [48246802]

+

35775

132628

...

...

...

...

......

...

26

chrX

[48270193], [48270307]

-

35778

132637

27

chrX

[48269421], [48269516]

-

35778

132636

28

chrX

[48267508], [48267557]

-

35778

132635

29

chrX

[48262894], [48262998]

-

35778

132633

30

chrX

[48261524], [48262111]

-

35778

132632


Typical biological data coerced into a data frame: a GRanges table representing genes SSX4 and SSX4B. One row represents one exon, seqnames indicates the chromosome name, ranges indicates the interval of exons, strand is the direction, tx_id and exon_id are the internal ids used for mapping cross-database.

Yin et al. Genome Biology 2012 13:R77   doi:10.1186/gb-2012-13-8-r77

Open Data