Description Usage Arguments Details Value Author(s) References See Also Examples
Construct a model-based binding profile as described in Reference (1).
1 2 3 4 5 | generate.binding.profile(fragment.distrib = function(x, ...) dgamma(x,
shape = 6, scale = 50), bs.size = 1, tile.size = 50, min.frag.size = 0,
positions = seq(0, 1001, by = 50), intensity.scaling = function(x, ...)
x, hybridization.prob = function(x, ...) as.integer(x > 10), interp = T,
plot = F, verbose = F, no.multicore=T, ...)
|
fragment.distrib |
Distribution of DNA fragment lengths. |
bs.size |
Footprint of TF binding site on the genome. |
tile.size |
Length of the array probes (in bp). |
min.frag.size |
Cutoff for minimum DNA fragment size. |
positions |
The distances from the center of the profile for which to compute the relative intensity. A longer vector increases the running time of this procedure. Values for distances other than those listed here are computed via interpolation. See 'interp'. |
intensity.scaling |
Intensity of DNA fragments as a function of their length. |
hybridization.prob |
Hybridization probability as a function of length of complementary sequence. |
interp |
If TRUE, interpolate the values for distances other than those listed in 'positions'. |
plot |
If TRUE, plot the resulting profile. |
verbose |
If TRUE, be verbose. |
no.multicore |
Prevent use of multiple cores, even if 'multicore' is installed. |
... |
Further parameters for 'fragment.distrib', 'intensity.scaling', and 'hybridization.prob'. |
No details.
A two-column matrix containing positions (distance from center, in bp) and relative intensities of the profile.
David J Reiss, Institute for Systems Biology
Maintainer: <dreiss@systemsbiology.org>
(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.
chip.deconv, deconv.entire.genome, fit.peak.profile, generate.fake.data, MeDiChI-data
1 2 3 4 5 6 7 | ## Compare profiles for DNA fragment distrs. with mean=300 and 400 bp.
kern.300 <- generate.binding.profile( fragment=function(x) dgamma( x,
shape=6, scale=50 ), verbose=TRUE )
kern.400 <- generate.binding.profile( fragment=function(x) dgamma( x,
shape=8, scale=50 ), verbose=TRUE )
plot( kern.300, typ="l", col="red" )
lines( kern.400, col="green" )
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.