spp (version 1.16.0)

get.smoothed.tag.density: Calculate chromosome-wide profiles of smoothed tag density

Description

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.

Usage

get.smoothed.tag.density(signal.tags, 
  control.tags = NULL, 
  bandwidth = 150, 
  bg.weight = NULL, 
  tag.shift = 146/2, 
  step = round(bandwidth/3),
  background.density.scaling = T,
  rngl = NULL, 
  scale.by.dataset.size = F)

Arguments

signal.tags

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

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. get.binding.characteristics()$peak$x/2)

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

Value

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.

See Also

writewig

Examples

# 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");
    
# }