cgEx: Sample chr22 Data

In hansenlab/bnbc: Bandwise normalization and batch correction of Hi-C data

Sample chr22 Data

Description

This is a sample ContactGroup object representing observations on chr22 from 3 1k Genomes trios' lymphoblastoid cell lines (LCL). colData(cgEx) gives the cell line name (CellLine), the ethnicity of the individual (Population), the family (Family), the gender (Gender), the relationship of the individuals within a trio (Role), the replicate number (Tech) and each sample's batch (Batch).

These data were generated by the dilution Hi-C method using HindIII (Lieberman-Aiden et al.). Hi-C contact matrices were generated by tiling the genome into 40kb bins and counting the number of interactions between bins.

These data have undergone no preprocessing.

Format

The data is an object of class ContactGroup.

Source

Raw data are available from the 4D nucleome data portal (https://data.4dnucleome.org) under accessions 4DNESYUYFD6H, 4DNESVKLYDOH, 4DNESHGL976U, 4DNESJ1VX52C, 4DNESI2UKI7P, 4DNESTAPSPUC, 4DNES4GSP9S4, 4DNESJIYRA44, 4DNESE3ICNE1.

References

Lieberman-Aiden, E, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.1181369")}

See Also

ContactGroup

hansenlab/bnbc documentation built on Feb. 4, 2024, 7:20 a.m.