addArchRGenome: Add a globally defined genome to all ArchR functions.

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Add a globally defined genome to all ArchR functions.

Description

This function will set the genome across all ArchR functions.

Usage

addArchRGenome(genome = NULL, install = TRUE)

Arguments

genome

A string indicating the default genome to be used for all ArchR functions. Currently supported values include "hg19","hg38","mm9", and "mm10". This value is stored as a global environment variable, not part of the ArchRProject. This can be overwritten on a per-function basis using the given function's geneAnnotationand genomeAnnotation parameter. For something other than one of the currently supported, see createGeneAnnnotation() and createGenomeAnnnotation().

install

A boolean value indicating whether the BSgenome object associated with the provided genome should be automatically installed if it is not currently installed. This is useful for helping reduce user download requirements.

GreenleafLab/ArchR documentation built on Feb. 28, 2024, 4:17 p.m.