s2: Sample binding site and related data from S2 and BG3 cell...

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

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.

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.