make_haplotypes-method: Split samples from a genind object into pseudo-haplotypes

In grunwaldlab/poppr: Genetic Analysis of Populations with Mixed Reproduction

Split samples from a genind object into pseudo-haplotypes

Description

Split samples from a genind object into pseudo-haplotypes

Usage

make_haplotypes(gid)

Arguments

gid	a genind or genlight object.

Details

Certain analyses, such as amova work best if within-sample variance (error) can be estimated. Practically, this is performed by splitting the genotypes across all loci to create multiple haplotypes. This way, the within-sample distance can be calculated and incorporated into the model. Please note that the haplotypes generated are based on the order of the unphased alleles in the genind object and do not represent true haplotypes.

Haploid data will be returned un-touched.

Value

a haploid genind object with an extra strata column called "Individual".

Note

The other slot will not be copied over to the new genind object.

See Also

poppr.amova() pegas::amova() as.genambig()

Examples

# Diploid data is doubled -------------------------------------------------

data(nancycats)
nan9 <- nancycats[pop = 9]
nan9hap <- make_haplotypes(nan9) 
nan9              # 9 individuals from population 9
nan9hap           # 18 haplotypes
strata(nan9hap)   # strata gains a new column: Individual
indNames(nan9hap) # individuals are renamed sequentially


# Mix ploidy data can be split, but should be treated with caution --------
# 
# For example, the Pinf data set contains 86 tetraploid individuals, 
# but there appear to only be diploids and triploid genotypes. When 
# we convert to haplotypes, those with all missing data are dropped.
data(Pinf)
Pinf
pmiss <- info_table(Pinf, type = "ploidy", plot = TRUE)

# No samples appear to be triploid across all loci. This will cause
# several haplotypes to have a lot of missing data.
p_haps <- make_haplotypes(Pinf)
p_haps
head(genind2df(p_haps), n = 20)

grunwaldlab/poppr documentation built on March 18, 2024, 11:24 p.m.