Description Usage Arguments Value See Also Examples
Given signal and control tag positions, the method calculates log2 signal to control enrichment esimates (maximum likelihood) for each chromosome, based on the smoothed tag density profile (see get.smoothed.tag.density).
1 2 3 4 5 6 7 8 9 | get.smoothed.enrichment.mle(signal.tags,
control.tags,
tag.shift = 146/2,
background.density.scaling = F,
pseudocount = 1,
bg.weight = NULL,
rngl = NULL,
chrl = NULL,
...)
|
signal.tags |
signal chromosome tag coordinate vectors (e.g. output
of |
control.tags |
control (input) tags |
tag.shift |
number of base pairs by which positive and negative tag coordinates should be shifted towards eachother (half of binding peak separation distance) |
background.density.scaling |
background.density.scaling |
pseudocount |
pseudocount value to be added to tag density - defaults to 1 |
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. |
rngl |
rngl |
chrl |
chrl |
... |
additional parameters should be the same as those passed
to the |
A list of elements corresponding to chromosomes, with each element being an $x/$y data.frame giving the position and associated log2 signal/control enrichment estimate.
1 2 3 4 5 6 7 | ## Not run:
# get smoothed enrichment estimate profile using 500bp bandwidth at
# 50bp steps
smoothed.M <- get.smoothed.enrichment.mle(chip.data,bandwidth=500,step=50);
writewig(smoothed.M,"example.smoothedM.wig","Example smoothed log2 intensity ratio estimate");
## End(Not run)
|
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