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

Description Usage Arguments Details Value Author(s) See Also

View source: R/annotation.R

Description

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

Usage

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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, favorov@sensi.org

See Also

differential.coverage


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