makeScheme: Automate a GbsrScheme object building.

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

Automate a GbsrScheme object building.

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 automates the building of a GbsrScheme object.

Usage

makeScheme(object, generation, crosstype, ...)

## S4 method for signature 'GbsrGenotypeData'
makeScheme(object, generation, crosstype)

Arguments

object	A GbsrGenotypeData object.
generation	An integer to indicate which generation of selfing or sibling-crossing your population is.
crosstype	A string to indicate the type of cross conducted with a given generation.
...	Unused.

Details

A scheme object is just a data.frame indicating a population size 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 crosstype specified to makeScheme() can take "selfing" and "sibling". When your population has $2^n$ parents specified by setParents(), makeScheme() assumes those parents were crossed in the "funnel" design in which $2^n$ parents are crossed to obtain $2^n/2$ F1 hybrids followed by successive intercrossings (pairings) of the hybrids to combine the genomes of all parents in one family of siblings. The makeScheme() function assumes that the parents that were assigned an odd number member ID (N) in setParents() had been crossed with the parent that were assigned an even number (N+1). For example, if you set parents as shown below. The makeScheme() function prepare a scheme information that indicates the intercrossings of "p1 x p2", "p3 x p4", "p5 x p6", and "p7 x p8" followed by crossing of "p1xp2_F1 x p3xp4_F1" and "p5xp6_F1 x p7xp8_F1" and then crossing of the two 4-way crossed liens to produce 8-way crossed hybrid lines. If, for example, generation = 5 indicating an F5 generation was specified to makeScheme(), the function adds 4 successive selfing or sibling crossings in the scheme. The created GbsrScheme object will be set in the scheme slot of the GbsrGenotypeData object.

Value

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

See Also

initScheme(), 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"))

gds <- makeScheme(gds, generation = 2, 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 Sept. 14, 2024, 4:47 p.m.