linkdf_shortcut: Linkdf shortcut

In Alethere/SmoothDescent: Application of map-based genotype correction algorithm Smooth Descent

Linkdf shortcut

Description

Shortcut to calculate the linkage data.frame using polymapR's approach to autopolyploid linkage calculation. Random pairing is assumed, it only considers one linkage group at a time and returns linkage both from parent1 to parent2 and viceversa. Importantly, markers for which parental genotype does not match offspring segregation are eliminated.

Usage

linkdf_shortcut(geno, ploidy, p1name, p2name, ncores = 1)

Arguments

geno	numeric data.frame or matrix, with marker names as rownames and individual names as column names.
ploidy	numeric, ploidy of both parents.
p1name	character, name of the first parent.
p2name	characther, name of the second parent.
ncores	numeric, number of threads to use in the linakge calculation.

Value

a linkage dataframe. Some estimates might be duplicated, since they are calculated for both parents.

Alethere/SmoothDescent documentation built on Oct. 21, 2023, 7:11 a.m.