bre80: Bre80 Cell Line

In chicane: Capture Hi-C Analysis Engine

Description

A dataset containing processed data from a capture Hi-C experiment in the Bre80 normal epithelial breast tissue cell line. The experiment targeted several breast cancer risk loci, and reads that mapped to the 2q35 SNPs rs13387042 and rs16857609 are included in the dataset.

Data was prepared using the prepare.data function. Coordinates are GRCh38.

Usage

data(bre80)

Format

A data table object with 47,766 rows and 13 columns.

The variables are as follows:

• target.id String in chrN:start-end format identifying target fragment

• bait.id String in chrN:start-end format identifying bait fragment

• target.chr Chromosome of target fragment

• target.start Start coordinate of target fragment (zero-based)

• target.end End coordinate of target fragment

• bait.chr Chromosome of bait fragment

• bait.start Start coordinate of bait fragment (zero-based)

• bait.end End coordinate of bait fragment

• bait.to.bait Boolean indicating if the interaction is bait-to-bait (i.e. the fragment listed as target is also a bait)

• bait.trans.count The number of reads linking the bait to fragments in trans (a measure of "interactibility")

• target.trans.count The number of reads linking the target to fragments in trans (a measure of "interactibility")

• distance Distance between the midpoints of the bait and target fragments (basepairs). NA for trans interactions

• count The number of reads linking the two fragments

References

Baxter, Joseph S., et al. "Capture Hi-C identifies putative target genes at 33 breast cancer risk loci." Nature Communications 9.1 (2018): 1028.

chicane documentation built on Nov. 7, 2021, 1:07 a.m.