GbsrScheme-class: Class 'GbsrScheme'

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

Class GbsrScheme

Description

GBScleanR uses breeding scheme information to set the expected number of cross overs in a chromosome which is a required parameter for the genotype error correction with the hidden Markov model implemented in the estGeno() function. This class stores those information including ID of parental samples, type crosses performed at each generation of breeding and population sizes of each generation. This class is not exported.

Slots

crosstype

A vector of strings indicating the type of crossing done at each generation.

mating

A list of matrices showing combinations member IDs of samples mated.

parents

A vector of member IDs of parents.

progenies

A vector of memeber IDs of progenies produced at each generation.

samples

A vector of member IDs of samples indicating which samples are derived from which pedigrees.

See Also

GbsrGenotypeData dnd loadGDS().

Examples

# `loadGDS()` initialize a `GbsrScheme` object internally and
# attache it to the shceme slot of a [GbsrGenotypeData] object.

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

# Print the information stored in the `GbsrScheme` object.
showScheme(gds)

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

tomoyukif/GBScleanR documentation built on March 12, 2024, 6:27 a.m.