setReplicates: Set identifiers to indicates which samples are replicates.

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

Set identifiers to indicates which samples are replicates.

Description

Not implemented yet. This function assign identifiers that indicates which samples are replicates those which should have the same genotypes at all markers.

Usage

setReplicates(object, replicates, ...)

## S4 method for signature 'GbsrGenotypeData'
setReplicates(object, replicates)

Arguments

object	A GbsrGenotypeData object.
replicates	A vector of integers, numbers, or characters to indicate grouping of samples as replicates.
...	Unused.

Details

The replicates of samples specified in setReplicates() will have the same genotypes at all markers in the estimated genotypes obtained via estGeno(). In the genotype estimation by estGeno(), the Viterbi scores for each possible genotype (haplotype) at each marker for the replicates will be replaced with the average score for the replicates.

Value

A GbsrGenotypeData object with genotype count information.

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)

gds <- setParents(gds, parents = c("Founder1", "Founder2"))

# When your data has 100 samples, two replicates for each offspring,
# and the samples are ordered as the 1st replicate followed by the 2nd
# replicate, you can specify replicates as below.
# gds <- setReplicates(gds, replicates = rep(1:50, each = 2))

# If you need to confirm the order of samples, run the following code.
# id <- getSamID(gds)

# Replicate IDs should be set also to parents. Therefore, please include

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

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