annotate: Classify all gene positions.
In coregenomics/nascentrna: Classify Nascent RNA Transcripts using Decision Tree

annotate is a convenience wrapper for running all other classification functions in this package using default values. See the package vignette for the decision tree used to determine the logical steps of classification.

da_tss tests for downstream-antisense TSS.

ua_rna tests for upstream-antisense RNA. The distance at which neighboring promoters appear is ~300 bp according to Fig 2d in Chen et al 2016 http://dx.doi.org/10.1038/ng.3616

enhancer tests for transcription regulatory elements outside of annotated genes.

annotate(tss, genes)

da_tss(tss, genes, min_start = 0, max_start = 300)

ua_rna(tss, genes, min_start = 0, max_start = 300)

enhancer(tre, genes)

`tss`	GRanges of experimentally found active gene region start sites to be classified.
`genes`	GRanges of known genes around which to classify `tss` regions.
`min_start`	Minimum integer distance away from gene start to find feature.
`max_start`	Maximum integer distance away from gene start to find feature.
`tre`	GRanges of experimentally found active putative transcription regulatory regions to be classified.

annotate returns GRanges of same size as tss with an additional class column of best position classification, and associated gene column of the corresponding gene.

da_tss returns a Hits object mapping gene with downstream-antisense TSS with a column for the tss query index (queryHits), genes subject index (subjectHits) and the distance between the pair.

ua_rna returns a Hits object mapping gene with downstream-antisense RNA with a column for the tss query index (queryHits), genes subject index (subjectHits) and the distance between the pair.

enhancer subsets tre to values outside genes.

coregenomics/nascentrna documentation built on May 7, 2019, 8:38 a.m.