getHaplotype: Get haplotype call data.

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

Get haplotype call data.

Description

Haplotype calls are retrieved from the GDS file linked to the given GbsrGenotypeData object.

Usage

getHaplotype(object, parents = FALSE, valid = TRUE, chr = NULL, ...)

## S4 method for signature 'GbsrGenotypeData'
getHaplotype(object, parents, valid, chr)

Arguments

object	A GbsrGenotypeData object.
parents	A logical value or "only" to include data for parents or to get data only for parents.
valid	A logical value. See details.
chr	A integer vector of indexes indicating chromosomes to get read count data.
...	Unused.

Details

Haplotype call data can be obtained from the "estimated.haplotype" node of the GDS file which can be generated via the estGeno() function. Thus, this function is valid only after having executed estGeno(). If valid = TRUE, read counts for only valid marker and valid samples will be obtained.

Value

An integer array of haplotype data. The array have 2 x M x N dimensions, where M is the number of markers and N is the number of samples. Each integer values represent the origin of the haplotype. For example, in the population with two inbred founders, values take either 1 or 2 indicating the hapotype descent from founder 1 and 2. If two outbred founders, values take 1, 2, 3, or 4 indicating the first and second haplotype in founder 1 and the first and second haplotype in founder 2.

See Also

estGeno()

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)

hap <- getHaplotype(gds)

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

tomoyukif/GBScleanR documentation built on Sept. 14, 2024, 4:47 p.m.