linkdf_shortcut: Linkdf shortcut

Description Usage Arguments Value

View source: R/mapping.R

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

1
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 Jan. 14, 2022, 9:40 p.m.