select.informative.tags: Choose informative tags

In spp: ChIP-Seq Processing Pipeline

Description

For datasets with tag alignment quality information (e.g. number of mismatches for Eland alignments), get.binding.characteristics determines whether inclusion of tags from each specific quality bin improves the cross-correlation profile. The present function is then used to actually select these informative tags, discarding all other information, including quality scores that are not used in further processing.

Usage

select.informative.tags(data, binding.characteristics)

Arguments

data	Full alignment data (a list with $tags and $quality elements)
binding.characteristics	result of a get.binding.characteristics call. If NULL value is supplied,all tags will be accepted.

Value

A chromosome-wise tag list. Each element of the list corresponds to a chromosome and is a numeric vector of 5' tag coordinates, with sign designating DNA strand. This form of tag data is used for most of the other processing.

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