get.broad.enrichment.clusters: Determine broad clusters of enrichment

In spp: ChIP-Seq Processing Pipeline

Description

Scan chromosomes with a pre-defined window size, comparing scaled ChIP and input tag coutns to see if their ratio exceeds that expected from a Poisson process (normalized for dataset size).

Usage

get.broad.enrichment.clusters(signal.data, 
  control.data, 
  window.size=1e3,
  z.thr=3,
  tag.shift=146/2,
  background.density.scaling = F,
  ...)

Arguments

signal.data	chip.tags, foreground tag vector list
control.data	input.tags, background tag vector list
window.size	window size to be used for tag counting
z.thr	Z-score to be used as a significance threshold
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	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.
...	additional parameters should be the same as those passed to the find.significantly.enriched.regions

Value

A list of elements corresponding to chromosomes, with each element being an $s/$e/$rv data.frame giving the starting, ending positions and the log2 enrichment estimate for that region.

spp documentation built on May 30, 2019, 5:03 p.m.