setup_locusdef: Function to setup locus definitions

In chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Description

Function to setup locus definitions

Usage

setup_locusdef(ldef_code, genome, randomization = NULL)

Arguments

ldef_code	One of 'nearest_tss', 'nearest_gene', 'exon', 'intron', '1kb', '1kb_outside', '1kb_outside_upstream', '5kb', '5kb_outside', '5kb_outside_upstream', '10kb', '10kb_outside', '10kb_outside_upstream'. Alternately, a file path for a custom locus definition. NOTE: Must be for a supported_genome(), and must have columns 'chr', 'start', 'end', and 'gene_id', or 'geneid'.
genome	One of the supported_genomes().
randomization	One of NULL, 'complete', 'bylength', or 'bylocation'. See the Randomizations section in ?chipenrich. Default NULL.

Value

A list with components ldef and tss.

chipenrich documentation built on Nov. 8, 2020, 8:11 p.m.