setParents: Set labels to samples which should be recognized as parents...

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

Set labels to samples which should be recognized as parents of the population to be subjected to error correction.

Description

Specify two or more samples in the dataset as parents of the population. Markers will be filtered out up on your specification.

Usage

setParents(object, parents, nonmiss = FALSE, mono = FALSE, bi = FALSE, ...)

## S4 method for signature 'GbsrGenotypeData'
setParents(object, parents, nonmiss, mono, bi)

Arguments

object	A GbsrGenotypeData object.
parents	A vector of strings with at least length two. The specified strings should match with the samples ID available via getSamID().
nonmiss	A logical value whether to filter out markers which are missing in parents.
mono	A logical value whether to filter out markers which are not monomorphic in parents.
bi	A logical value whether to filter out marekrs which are not biallelic between parents.
...	Unused.

Details

The clean function of GBScleanR uses read count information of samples and their parents separately to estimate most probable genotype calls of them. Therefore, you must specify proper samples as parents via this function. If you would like to remove SNP markers which are not biallelic and/or not monomorphic in each parent, set mono = TRUE and bi = TRUE. The replicates of parental samples specified to the repliate argument of setParents() 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 at each marker for the replicates will be replaced with the average score for the replicates.

Value

A GbsrGenotypeData object with parents 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)

# Find the IDs of parental samples.
parents <- grep("Founder", getSamID(gds), value = TRUE)

# Set the parents and flip allele information
# if the reference sample (Founder1 in our case) has homozygous
# alternative genotype at some markers of which alleles will
# be swapped to make the reference sample have homozygous
# reference genotype.
gds <- setParents(gds, parents = parents)

# Initialize a scheme object stored in the slot of the GbsrGenotypeData.
# We chose `crosstype = "pair"` because two inbred founders were mated
# in our breeding scheme.
# We also need to specify the mating matrix which has two rows and
# one column with integers 1 and 2 indicating a sample (founder)
# with the memberID 1 and a sample (founder) with the memberID 2
# were mated.
gds <- initScheme(gds, mating = cbind(c(1:2)))

# Add information of the next cross conducted in our scheme.
# We chose 'crosstype = "selfing"', which do not require a
# mating matrix.
gds <- addScheme(gds, crosstype = "selfing")

# Execute error correction by estimating genotype and haplotype of
# founders and offspring.
gds <- estGeno(gds)

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

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