site.merge: Cluster close-by sites into consensus sites
In DBChIP: Differential Binding of Transcription Factor with ChIP-seq

Description Usage Arguments Details Value See Also

Cluster close-by sites into consensus sites through agglomerative (bottom-up) hierarchical clustering.

1	site.merge(bs.list, in.distance = 100, out.distance = 250)

`bs.list`	internal format of binding site. Result of `read.binding.site.list`.
`in.distance`	within cluster distance. If the distance between centroids of two clusters are smaller than this value, the clusters will be merged into one. Default value 100 bp.
`out.distance`	out of cluster distance. If the distance between centroids of two clusters are larger than this value, they are considered different binding sites. Default value 250 bp.

We group predicted locations from multiple conditions into clusters of close-by locations by using agglomerative (bottom-up) hierarchical clustering with centroid linkage.

If the distance between centroids of two clusters are between in.distance and out.distance, the cluster with higher weight will be kept.

A list where each element represents a chromosome. Within each chromosome, it is a data.frame with following fields

`pos`	consensus binding position.
`nsig`	number of significant original binding sites that are merged into consensus site.
`origin`	the origin of merged binding sites.
`ori.pos`	the original positions of merged binding sites. The consensus position is a weighted average of original positions.