Description Usage Arguments Value See Also Examples
Given tag positions, the method calculates for each chromosome a tag density profile, smoothed by the Gaussian kernel. If the optional control tags are provided, the difference between ChIP and control tag density is returned.
1 2 3 4 5 6 7 8 9 |
signal.tags |
signal chromosome tag coordinate vectors (e.g. output
of |
control.tags |
optional control (input) tags |
bandwidth |
standard deviation of the Gaussian kernel |
bg.weight |
optional weight by which the background density should be multipled for scaling. If not supplied, the weight is calculated based on the ratio of the reduced ChIP to input dataset sizes. |
tag.shift |
Distance by which the positive and negative strand
tags should be shifted towards eachother. This
normally corresponds to the half of the cross-correlation peak
position (e.g. |
step |
The distance between the regularly spaced points for which the values should be calculated. |
background.density.scaling |
If TRUE, regions of significant tag enrichment will be masked out when calculating size ratio of the signal to control datasets (to estimate ratio of the background tag density). If FALSE, the dataset ratio will be equal to the ratio of the number of tags in each dataset. |
rngl |
rngl |
scale.by.dataset.size |
scale.by.dataset.size |
A list of elements corresponding to chromosomes, with each element
being an $x/$y data.frame giving the position and associated tag
density. Use writewig
to output the structure to a WIG
file.
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
smoothed.density <- get.smoothed.tag.density(chip.data,
control.tags=input.data,
bandwidth=200,
step=100,
tag.shift=round(binding.characteristics$peak$x/2));
writewig(smoothed.density,
"example.density.wig",
"Example smoothed, background-subtracted tag density");
## End(Not run)
|
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