setup_mappa: Function to setup mappability

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

Description

Function to setup mappability

Usage

setup_mappa(mappa_code, genome, ldef_code, ldef_obj)

Arguments

mappa_code	One of NULL, a file path to a custom mappability file, or an integer for a valid read length given by supported_read_lengths. If a file, it should contain a header with two column named 'gene_id' and 'mappa'. Gene IDs should be Entrez IDs, and mappability values should range from 0 and 1. Default value is NULL.
genome	One of the supported_genomes().
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'.
ldef_obj	A LocusDefinition object.

Value

A data.frame with columns gene_id and mappa.

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