genes.intersected.by.interval: genes.intersected.by.interval
In favorov/differential.coverage: Differential Coverage package

Description Usage Arguments Details Value Author(s) See Also

Generates a list of genes (possibly, empty) that intersects with each interval

genes.intersected.by.interval(
  noodles,
  flanks = 0,
  genes = NA,
  genome.id = "gencode19"
)

`noodles`	the `GRanges` list of intervals to look TSS in
`flanks`	lenght to inflate the noddles by before the search; if >0, the seqlengths information is to be set in `noodles`
`genes`	it is GRandes oject with the annotation genes. The gene_name matadata field is almost required, it passes the gene name to form output. The default is NA that means that the function will call `get.Known.Gene.List`
`genome.id`	is genome.annotation.id to call `get.Known.Gene.List`

After the noodles (the set of intervals to search intersections with) are inflated by flanks, we look for all the genes that overlap with the (inflated) intervals. Genes are provided by parameter or they are returned by get.Known.Gene.List for genome_id. If a noodle (interval) overlaps more that one gene, we form a text list of the genes.

GRanges object, noodles argument with added gene-overlapped genes for each interval

Alexander Favorov, favorov@sensi.org

differential.coverage

favorov/differential.coverage documentation built on Feb. 18, 2022, 5:50 p.m.