genes.with.TSS.covered.by.interval: genes.with.TSS.covered.by.interval

In favorov/differential.coverage: Differential Coverage package

Description

Generates a list of genes (possibly, empty) that start inside each interval

Usage

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

Arguments

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

Details

After the noodles (the set of intervals to search TSS in) are inflated by flanks, we look for all the TSS that start inside 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 TSS, we form a text list of the genes.

Value

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

Author(s)

Alexander Favorov, [e-mail]

See Also

differential.coverage

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