read_ldef: Function to read custom locus definition from file

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

Description

This function reads a tab-delimited text (with a header) file that should have columns 'chr', 'start', 'end', and a column named 'gene_id' (or 'geneid') with the Entrez Gene ID. If a supported_genomes() is given, then a column of gene symbols named 'symbol', will be added. If an unsupported genome is used there are two options: 1) Have a column named 'symbols' with the gene symbols in the custom locus definition, and leave genome = NA, or 2) leave genome = NA, do not provide gene symbols, and NAs will be used.

Usage

read_ldef(file_path, genome = NA)

Arguments

file_path	A file path for the custom locus definition.
genome	A genome from supported_genomes(), default NA.

Value

A LocusDefinition class object with slots dframe, granges, genome.build, and organism.

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