IMR90_DNAloops_pairs: plotgardener example DNA loop pair data

In PhanstielLab/plotgardenerData: Datasets and test data files for the plotgardener package

plotgardener example DNA loop pair data

Description

A dataset listing interaction data along genomic coordinates in the region chr21:28000000-30300000 according to the hg19 genome build. This data represents called DNA loops in the IMR90 cell line.

Usage

data("IMR90_DNAloops_pairs")

Format

a dataframe in BEDPE (paired ranges) format

chrom1

The name of the chromosome on which the first end of the feature exists.

start1

The starting position of the first end of the feature on chrom1.

end1

The ending position of the first end of the feature on chrom1.

chrom2

The name of the chromosome on which the second end of the feature exists.

start2

The starting position of the second end of the feature on chrom2.

end2

The ending position of the second end of the feature on chrom2.

References

Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014 Dec 18;159(7):1665-80. doi: 10.1016/j.cell.2014.11.021. Epub 2014 Dec 11. Erratum in: Cell. 2015 Jul 30;162(3):687-8. PMID: 25497547; PMCID: PMC5635824. (PubMed)

PhanstielLab/plotgardenerData documentation built on June 15, 2024, 10:38 p.m.