upgr: generate GRanges of upstream regions

In gonzolgarcia/svpluscnv: Integrative analyses of CNV segmentation and SV variant calls

Description

generate GRanges of upstream regions

Usage

upgr(ggr, upstr = 50000)

Arguments

ggr	(S4) a GenomicRanges object containing gene annotations. It is crutial that the genome version 'genesgr' and the input 'sv' are the same. The GRanges object must contain 'strand' and a metadata field 'gene_id' with unique values. Seqnames are expected in the format (chr1, chr2, ...).
upstr	(numeric) size in base pairs to define gene upstream region onto which breakpoint overlaps will be identified. The strand value, start and stop positions defined in genesgr will be used to create a GRanges object of upstream regions.

Value

(S4) aa GRanges object of upstream regions

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.