genes.intersected: genes.intersected

Description Usage Arguments Details Value Author(s) See Also

View source: R/annotation.R

Description

Generates list of genes that intersect a given set of intervals

Usage

1
genes.intersected(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 intersection with) are inflated by flanks, we look for all the genes that intersect the (inflated) intervals. Genes are provided by parameter or they are returned by get.Known.Gene.List for genome_id. If the noodles has p.value and/or fdr metadata, we ascribe the data of the interval to the retrieved gene. If there a gene refers to a set of noodles, it has min ascribed. The ishyper data is also transferred to gene, if it is not contradictory.

Value

GRanges object that is the list of the genes we look for - the object is not co-indexed with noodles parameter

Author(s)

Alexander Favorov, favorov@sensi.org

See Also

differential.coverage


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