upgr: generate GRanges of upstream regions
In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

generate GRanges of upstream regions

1	upgr(ggr, upstr = 50000)

`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.

(S4) aa GRanges object of upstream regions

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.

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