GbsrGenotypeData-class: Class GbsrGenotypeData

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

Class GbsrGenotypeData

Description

The GbsrGenotypeData class is the main class of GBScleanR and user work with this class object.

Details

The GbsrGenotypeData class is an extention of SeqVarGDSClass-class in the SeqArray package to store summary data of genotypes and reads and a GbsrScheme object that contains mating scheme information of the given population.. The slots marker and sample store a data.frame object for variant-wise and sample-wise summary information, respectively. The scheme slot holds a GbsrScheme object. The function loadGDS() initialize the GbsrGenotypeData class.

Slots

marker

A data.frame object.

sample

A data.frame object.

scheme

A GbsrScheme object.

Examples

# [loadGDS()] initialize the [GbsrGenotypeData] object.

# Load a GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

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

tomoyukif/GBScleanR documentation built on June 1, 2025, 10:13 p.m.