MeDiChI-data: ChIP-chip data supporting the MeDiChI package

In MeDiChI: MeDiChI ChIP-chip deconvolution library

Description

Three different ChIP-chip datasets of varying tiling resolution, referenced in Reference (1) below.

Usage

data(halo.hires)
data(halo.lowres)
data(yeast.gcn4)

Format

The format of "halo.lowres" is: chr [1:3] "data.halo.lowres" "kernel.halo.lowres" "gene.coords" The format of "halo.hires" is: chr [1:3] "data.halo.hires" "kernel.halo.hires" "gene.coords" The format of "yeast.gcn4" is: chr [1:4] "data.yeast.gcn4" "kernel.yeast.gcn4" "kernel.yeast.gcn4.jbd" "gene.coords"

Details

"halo.lowres" loads:
"data.halo.lowres" – low-resolution HaloSpan Halobacterium sp. TfbD ChIP-chip data, formatted for input to chip.deconv() and deconv.entire.genome(). Data is described in ref. (1) below.
"kernel.halo.lowres" – deconvolution kernel learned for this data via fit.peak.profile().
"gene.coords" – map of gene coordinates for this organism for use in plotting functions.
"halo.hires" loads:
"data.halo.hires" – high-resolution Nimblegen format Halobacterium sp. TfbD ChIP-chip data, formatted for input to chip.deconv() and deconv.entire.genome(). Data is described in ref. (1) below.
"kernel.halo.hires" – deconvolution kernel for this data via fit.peak.profile().
"gene.coords" – map of gene coordinates for this organism for use in plotting functions.
"yeast.gcn4" loads:
"data.yeast.gcn4" – 266bp-resolution S. cerevisiae Gcn4 ChIP-chip data, formatted for input to chip.deconv() and deconv.entire.genome(). Data is described in ref. (1) below.
"kernel.yeast.gcn4" – deconvolution kernel for this data via fit.peak.profile().
"kernel.yeast.gcn4.jbd" – deconvolution kernel used by ref. (2) for the JBD algorithm.
"gene.coords" – map of gene coordinates for this organism for use in plotting functions.

Source

See references below.

References

(1). Reiss, DJ and Facciotti, MT and Baliga, NS. (2007). "Model-based deconvolution of genome-wide DNA binding", Bioinformatics; doi: 10.1093/bioinformatics/btm592. http://baliga.systemsbiology.net/medichi
(2) Qi, Y and et al. (2006). "High-resolution computational models of genome binding events", Nature Biotechnol, 24(8), 963-970. http://cgs.csail.mit.edu/jbd.

See Also

chip.deconv, deconv.entire.genome, fit.peak.profile, generate.fake.data, generate.binding.profile

Examples

data(halo.hires)

## Then try print(data.halo.lowres) to see the format.

data(halo.lowres)
data(yeast.gcn4)

MeDiChI documentation built on May 2, 2019, 5:32 p.m.