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haplotype object store specific information of individuals haplotype

Public fields

SNPinfo

[SNPinfo class] information about the haplotype of the SNPs (see:SNPinfo)

values

[list] list haplotype values

Active bindings

allelDose

[numeric] vector of genotypes encoded in allele dose

Methods


Method new()

Create a new Haplotype object.

Usage

haplotype$new(SNPinfo, haplo)

Arguments

SNPinfo

[SNPinfo class] information about the haplotype's SNPs (see:SNPinfo)

haplo

[matrix] named matrix of the haplotypes for all markers. This matrix should have `SNPinfo$specie$ploidy` line and `SNPinfo$nSNP()` columns.

Returns

A new `haplotype` object.

Examples

# create specie
mySpec <- specie$new(nChr = 3,
                     lchr = c(100, 150, 200),
                     lchrCm = 100,
                     verbose = FALSE)

# simulate SNP
SNPcoord <- data.frame(chr = c(rep("Chr1", 3),
                               rep("Chr2", 4),
                               rep("Chr3", 5)),
                       physPos = c(sample(100, 3),
                               sample(150, 4),
                               sample(200, 5)),
                       linkMapPos = NA,
                       SNPid = sprintf(fmt = paste0("SNP%0", 2,"i"),
                                       1:(3 + 4 + 5)))

# create SNPinfo object
SNPs <- SNPinfo$new(SNPcoord = SNPcoord, specie = mySpec)
# simulate haplotype
rawHaplo <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                   nrow = 2)
colnames(rawHaplo) <- sprintf(fmt = paste0("SNP%0", 2,"i"),
                              1:(3 + 4 + 5))
haplo <- haplotype$new(SNPinfo = SNPs,
                       haplo = rawHaplo)


Method clone()

The objects of this class are cloneable with this method.

Usage

haplotype$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `haplotype$new`
## ------------------------------------------------

# create specie
mySpec <- specie$new(nChr = 3,
                     lchr = c(100, 150, 200),
                     lchrCm = 100,
                     verbose = FALSE)

# simulate SNP
SNPcoord <- data.frame(chr = c(rep("Chr1", 3),
                               rep("Chr2", 4),
                               rep("Chr3", 5)),
                       physPos = c(sample(100, 3),
                               sample(150, 4),
                               sample(200, 5)),
                       linkMapPos = NA,
                       SNPid = sprintf(fmt = paste0("SNP%0", 2,"i"),
                                       1:(3 + 4 + 5)))

# create SNPinfo object
SNPs <- SNPinfo$new(SNPcoord = SNPcoord, specie = mySpec)
# simulate haplotype
rawHaplo <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                   nrow = 2)
colnames(rawHaplo) <- sprintf(fmt = paste0("SNP%0", 2,"i"),
                              1:(3 + 4 + 5))
haplo <- haplotype$new(SNPinfo = SNPs,
                       haplo = rawHaplo)