get_great_regions: Generate regions similar to GREAT based on the UCSC RefGenes...
In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description Usage Arguments Details Value

GREAT is the [Genomic Regions Enrichment of Annotations Tool](http://great.stanford.edu).

1 2	get_great_regions(symbols = NULL, minexpand = 5000, maxexpand = 1e+06, genome = "mm10")

`symbols`	A character object with gene symbols to retain. If NULL, will return all genes. Default is NULL.
`minexpand`	Minimum distance from the TSS to expand. This region will be retained even if it overlaps an adjacent gene. Default is 5000.
`maxexpand`	Maximum distance from the TSS to expand. This region will be bounded by adjacent minimum regions of the nearest gene.
`genome`	The genome to use. Default is "mm10".

GREAT regions have a minimum size around the TSS. In the real deal, this is an asymmetrical region (more upstream than downstream), but in this implementation, the minimum region specified by minexpand is symmetrical. Regions then expand up to the maximum distance or until they hit the minimum region of an adjacent gene, whichever is smaller.

a data.frame with columns matching BED format (chr, start, end, name, score, and strand).

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.