linkage_diseq: Computes the linkage disequilibrium for a set of sequences

In philliplab/yasss: Yet Another Short Sequence Simulator

Description

Computes the linkage disequilibrium for a set of sequences

Usage

linkage_diseq(seqs, min_prev = 0.2, max_prev = 0.8, verbose = FALSE)

Arguments

seqs	The sequences on which the linkage disequilibrium is to be computed
min_prev	The minimum prevalence the majority variant must attain to be considered for inclusion. (This cutoff will not see much action)
max_prev	Majoritity variants with prevalences higher than this will not be considered.
verbose	Should intermediate results be included in the return value?

Value

A list with multiple elements:

• linkage The linkage scores for various distances and starting positions.

• cmat The consensusMatrix. Only included if verbose is specified.

philliplab/yasss documentation built on Sept. 7, 2020, 3:28 p.m.