genclone-class: GENclone and SNPclone classes

In poppr: Genetic Analysis of Populations with Mixed Reproduction

GENclone and SNPclone classes

Description

GENclone is an S4 class that extends the genind object.
SNPclone is an S4 class that extends the genlight object.

They will have all of the same attributes as their parent classes, but they will contain one extra slot to store extra information about multilocus genotypes.

Details

The genclone and snpclone classes will allow for more optimized methods of clone correction.

Previously for genind and genlight objects, multilocus genotypes were not retained after a data set was subset by population. The new mlg slot allows us to assign the multilocus genotypes and retain that information no matter how we subset the data set. This new slot can either contain numeric values for multilocus genotypes OR it can contain a special internal MLG class that allows for custom multilocus genotype definitions and filtering.

Slots

mlg

a vector representing multilocus genotypes for the data set OR an object of class MLG.

Extends

The genclone class extends class "genind", directly.
The snpclone class extends class "genlight", directly.

Note

When calculating multilocus genotypes for genclone objects, a rank function is used, but calculation of multilocus genotypes for snpclone objects is distance-based (via bitwise.dist and mlg.filter). This means that genclone objects are sensitive to missing data, whereas snpclone objects are insensitive.

Author(s)

Zhian N. Kamvar

See Also

as.genclone as.snpclone genind genlight strata setPop MLG mll mlg.filter

Examples

## Not run: 

# genclone objects can be created from genind objects
#
data(partial_clone)
partial_clone
(pc <- as.genclone(partial_clone))

# snpclone objects can be created from genlight objects
#
set.seed(999)
(gl <- glSim(100, 0, n.snp.struc = 1e3, ploidy = 2, parallel = FALSE))
(sc <- as.snpclone(rbind(gl, gl, parallel = FALSE), parallel = FALSE))
# 
# Use mlg.filter to create a distance threshold to define multilocus genotypes.
mlg.filter(sc, threads = 1L) <- 0.25
sc # 82 mlgs


## End(Not run)

poppr documentation built on March 31, 2023, 7:15 p.m.