initScheme: Build a GbsrScheme object

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

Build a GbsrScheme object

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 function build the object storing type crosses performed at each generation of breeding and population sizes.

Usage

initScheme(object, mating, ...)

## S4 method for signature 'GbsrGenotypeData'
initScheme(object, mating)

## S4 method for signature 'GbsrScheme'
initScheme(object, mating, parents)

Arguments

object	A GbsrGenotypeData object.
mating	An integer matrix to indicate mating combinations. The each element should match with IDs of parental samples which are 1 to N. see Details.
...	Unused.
parents	Indices of parental lines.

Details

A GbsrScheme object stores information of a population size, mating combinations and a type of cross applied to each generation of the breeding process to generate the population which you are going to subject to the estGeno() function. The first generation should be parents of the population. It is supposed that setParents() has been already executed and parents are labeled in the GbsrGenotypeData object. The number of parents are automatically recognized. The "crosstype" of the first generation can be "pairing" or "random" with pop_size = N, where N is the number of parents. You need to specify a matrix indicating combinations of mating, in which each column shows a pair of parental samples. For example, if you have only two parents, the mating matrix is mating = cbind(c(1:2)). The indices used in the matrix should match with the IDs labeled to parental samples by setParents(). The created GbsrScheme object is set in the scheme slot of the GbsrGenotypeData object.

Value

A GbsrGenotypeData object storing a GbsrScheme object in the "scheme" slot.

See Also

addScheme() and showScheme()

Examples

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

# Biparental F2 population.
gds <- setParents(gds, parents = c("Founder1", "Founder2"))

# setParents gave member ID 1 and 2 to Founder1 and Founder2, respectively.
gds <- initScheme(gds, mating = cbind(c(1:2)))

# Now the progenies of the cross above have member ID 3.
# If `crosstype = "selfing"` or `"sibling"`, you can omit a `mating` matrix.
gds <- addScheme(gds, crosstype = "self")

# Now you can execute `estGeno()` which requires a [GbsrScheme] object.

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

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