| bindingType
Specifying the criteria to associate peaks with annotation. Here is how to use it together with the parameter bindingRegion To obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = "startSite" and bindingRegion = c(-5000, 3000) To obtain peaks up to 5kb upstream within the gene body and 3kb downstream of gene/Exon End, set bindingType = "endSite" and bindingRegion = c(-5000, 3000) To obtain peaks from 5kb upstream to 3kb downstream of genes/Exons , set bindingType = "fullRange" and bindingRegion = c(-5000, 3000) To obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = "nearestBiDirectionalPromoters" and bindingRegion = c(-5000, 3000) startSite start position of the feature (strand is considered) endSite end position of the feature (strand is considered) fullRange whole range of the feature nearestBiDirectionalPromoters nearest promoters from both direction of the peaks (strand is considered). It will report bidirectional promoters if there are promoters in both directions in the given region (defined by bindingRegion). Otherwise, it will report the closest promoter in one direction. bindingRegion Annotation range used together with bindingType, which is a vector with two integer values, default to c (-5000, 5000). The first one must be no bigger than 0. And the sec ond one must be no less than 1. For details, see bindingType. ignore.peak.strand ignore the peaks strand or not. |
hg clone https://toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| annotate peaks by annoGR object in the given range | 0.1.0 | 16.01 | |