detect_ref_genome: Detect reference genome

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Detect reference genome

Description

Detect if the dataset was de novo or reference genome assembled

Usage

detect_ref_genome(chromosome = NULL, data = NULL, verbose = TRUE)

Arguments

chromosome	(string) String with chromosome ID, unique or not. Default: chromosome = NULL.
data	(optional, path or object) radiator GDS object or file. When this argument is used, the function look inside the GDS radiator node for: reference.genome node and TRUE/FALSE value markers.meta node and detect the information using the CHROM column chromosome node directly. Default: data = NULL.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Value

TRUE/FALSE if dataset is assembled with a reference genome or not.

Author(s)

Thierry Gosselin [e-mail]

Examples

## Not run: 
ref.genome <- radiator::detect_ref_genome(chromosome = tidy.data$CHROM)

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.