spp (version 1.16.0)

get.smoothed.enrichment.mle: Calculate chromosome-wide profiles of smoothed enrichment estimate

Description

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).

Usage

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, 
  ...)

Arguments

signal.tags

signal chromosome tag coordinate vectors (e.g. output of select.informative.tags

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 get.smoothed.tag.density, such as for example bandwidth (default value 150) and step (default value 50). see appropriate reference for get.smoothed.tag.density for details.

Value

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.

See Also

writewig

Examples

# 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");
  
# }