s2 {chroGPS} | R Documentation

## Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.

### Description

chroGPS example dataset including ChIP-CHIP (modEncode) and ChIP-Seq (NCBI GEO GSE19325) data for Drosophila melanogaster S2 and BG3 cell lines as well as S2 wildtype gene expression values coming from Affymetrix Drosophila2 arrays. The object `toydists` stores precomputed `distGPS` objects (called `d, d2, d3`) for the epigenetic factors used in the dynamic vignette that comes with the package. The objects `d.origs,m.origs`, contain the `distGPS` and `mds` objects for the 76 S2 epigenetic factors used in Font-Burgada et al. 2014, computed over modENCODE Origins of Replication at four different replication time points.

### Usage

    data(s2)
    data(s2Seq)
    data(bg3)
    data(repliSeq)

### Source

`http://www.modencode.org` `http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19325`

### References

`http://www.modencode.org` `http://www.ncbi.nlm.nih.gov/geo/`

### Examples

    data(s2)
    class(s2)
    s2
    s2names$Factor

    data(s2Seq)
    s2Seq

    data(bg3)
    names(bg3)

    data(repliSeq)
    class(d.origs)
    class(m.origs)
    names(d.origs)
    d.origs[[1]]
    m.origs[[1]]

    # See vignette examples for several uses of these datasets.

[Package chroGPS version 2.4.0 Index]