showScheme: Show the information stored in a GbsrScheme object

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

Show the information stored in a GbsrScheme object

Description

Print the information of each generation in a GbsrScheme object in the scheme slot of a GbsrGenotypeData object. 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.

Usage

showScheme(object, ...)

## S4 method for signature 'GbsrGenotypeData'
showScheme(object)

## S4 method for signature 'GbsrScheme'
showScheme(object, parents_name, pedigree)

Arguments

object	A GbsrGenotypeData object.
...	Unused.
parents_name	A vector of strings to indicate names of parental samples. This argument is used internally by showScheme() for the gbsrGenotypeData object.
pedigree	A integer vector indicating the member ID assignment to samples. This argument is used internally by showScheme() for the gbsrGenotypeData object.

Value

NULL. Print the scheme information on the R console.

See Also

initScheme() and addScheme()

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 April 27, 2024, 9:06 a.m.