loadGDS: Load a GDS file and construct a 'GbsrGenotypeData' object.

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Load a GDS file and construct a GbsrGenotypeData object.

Description

Load data stored in an input GDS file to R environment and create a GbsrGenotypeData instance. GBScleanR handles only one class GbsrGenotypeData and conducts all data manipulation via class methods for it.

Usage

loadGDS(x, load_filter = FALSE, ploidy = 2, verbose = TRUE)

Arguments

x	A string of the path to an input GDS file or a GbsrGenotypeData object to reload.
load_filter	A logical whether to load the filtering information made via setSamFilter() and setMarFilter() and saved in the GDS file via closeGDS() with save_filter = TRUE.
ploidy	Set the ploidy of the population.
verbose	if TRUE, show information.

Details

The first time to load a newly produced GDS file will take long time due to data reformatting for quick access. The GbsrGenotypeData object returned from loadGDS() can be also handled as SeqVarGDSClass of the SeqArray package.

Value

A GbsrGenotypeData object.

Examples

# Create a GDS file from a sample VCF file.
vcf_fn <- system.file("extdata", "sample.vcf", package = "GBScleanR")
gds_fn <- tempfile("sample", fileext = ".gds")
gbsrVCF2GDS(vcf_fn = vcf_fn, out_fn = gds_fn, force = TRUE)

# Load data in the GDS file and instantiate a `GbsrGenotypeData` object.
gds <- loadGDS(gds_fn)

# Reload data from the GDS file.
gds <- loadGDS(gds)

# Close the connection to the GDS file.
closeGDS(gds)

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.