MeDiChI-package: MeDiChI ChIP-chip deconvolution library

In MeDiChI: MeDiChI ChIP-chip deconvolution library

Description

Deconvolution of Chromatin-IP-to-microarray (ChIP-chip) data to identify binding sites at high resolution across the genome.
To be published in Bioinformatics and submitted to Bioconductor.
This package includes all data described in the manuscript.

Details

Package:	MeDiChI
Type:	Package
Version:	0.1-4
Date:	2007-11-25
License:	GPL version 3

demo(MeDiChI)

Author(s)

David J Reiss, Institute for Systems Biology

Maintainer: <[e-mail]>

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, MeDiChI-data, <lars>, <quadprog>, <Matrix>

Examples

demo( MeDiChI )

## Run the demo yourself:
data( "halo.lowres", package="MeDiChI" )

fit <- chip.deconv( data.halo.lowres, where="Chr", fit.res=30,
               center=650000, wind=20000, max.steps=100, n.boot=10,
               kernel=kernel.halo.lowres, verbose=TRUE, boot.sample.opt="case" )

coef( fit ) ## Print out the coefficients
plot( fit, plot.genes=TRUE, cex=0.5, cex.lab=0.8, cex.axis=0.8 ) 

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