cgEx: Sample chr22 Data
In bnbc: Bandwise normalization and batch correction of Hi-C data
Description
Format
Source
References
See Also
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
bnbc documentation built on Nov. 8, 2020, 8:15 p.m.
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Description Format Source References See Also
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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