assignScheme: Assign member IDs to samples

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

Assign member IDs to samples

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 assign member IDs to indicate which samples were derived from which pedigree that recorded in the GbsrScheme object.

Usage

assignScheme(object, id, ...)

## S4 method for signature 'GbsrGenotypeData'
assignScheme(object, id)

## S4 method for signature 'GbsrScheme'
assignScheme(object, id)

Arguments

object	A GbsrGenotypeData object.
id	A numeric vector indicating member IDs to assign to samples.
...	Unused.

Details

Member IDs can be shown by showScheme(). Only the member IDs assigned to progenies (not parents) are available to assign to samples. If the last generation recorded in the GbsrScheme object has only one member ID that should be assigned to all samples in your population, you can omit assigning IDs by assignScheme(). In that case, estGeno() automatically assign the only one member ID to all samples.

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

# The progeny of the selfing above has member ID 4.
# To execute genotype estimation for your samples, you need to assign a member
# ID to each of the samples.

# Check IDs of samples to be assigned member IDs if necessary.
getSamID(gds)

# The assignScheme() assign member IDs `id` to the samples in order.
# Please confirm the order of the member IDs in `id` and the order of the
# sample IDs shown by getSamID(gds).
gds <- assignScheme(gds, rep(4, nsam(gds)))

# If your population has samples all of which belong to only one pedigree,
# you can omit assignScheme() and let estGeno() automatically assign the
# last member ID to all samples.

############################################################################
# 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.