remove.local.tag.anomalies: Restrict or remove positions with too many tags relative to...
In spp: ChIP-Seq Processing Pipeline

Description Usage Arguments Value Note References

In Solexa ChIP-seq experiments some anomalous positions contain extremely high number of tags at the exact coordinates. The function scans the chromosomes, determining local tag density based on a provided window.size, doing two types of corrections: 1. removing all tags from positions that exceed local density by eliminate.fold; 2. reducing the tag count at positions exceeding cap.fold to the maximal allowed count. The statistical significance of counts exceeding either of these two threshold densities is calculated based on Poisson model, with confidence interval determined by the z.threshold Z-score parameter.

remove.local.tag.anomalies(tags, 
  window.size = 200, 
  eliminate.fold = 10, 
  cap.fold = 4, 
  z.threshold = 3)

`tags`	Chromosome-list of tag vectors
`window.size`	Size of the window used to assess local density. Increasing the window size considerably beyond the size of the binding features will result in flattened profiles, with bound positions exhibiting a difference of just 1 tag beyond the background.
`eliminate.fold`	Threshold definining fold-over background density above which the position is considered anomalous and removed completely.
`cap.fold`	Threshold fold-over background density above which the position is capped to the maximum statistically likely given local tag density
`z.threshold`	Z-score used to assess significance of a given position exceeding either of the two density thresholds.

A modified chromosome-wise tag vector list.

~~further notes~~ Increasing window.size to very large values will result in flat profiles similar to those described by Zhang et al. "Model-based Analysis of ChIP-Seq (MACS)." Genome Biol. 2008 Sep 17;9(9):R137.

~put references to the literature/web site here ~

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