cgEx {bnbc} | R Documentation

## 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. doi: 10.1126/science.1181369

### See Also

`ContactGroup`

[Package bnbc version 1.4.0 Index]