SNSN_LOD_deviations: Identify deviations in LOD scores between pairs of simplex x...

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

SNSN_LOD_deviations checks whether the LOD scores obtained in the case of pairs of simplex x nulliple markers are compatible with expectation. This can help identify problematic linkage estimates which can adversely affect marker clustering.

Usage

SNSN_LOD_deviations(linkage_df, ploidy, N, plot_expected = TRUE,
  alpha = c(0.05, 0.2), phase = c("coupling", "repulsion"))

Arguments

linkage_df	A linkage data.frame as output of linkage.
ploidy	Integer. The ploidy level of the species.
N	Numeric. The number of F1 individuals in the mapping population.
plot_expected	Logical. Plot the observed and expected relationship between r and LOD.
alpha	Numeric. Vector of upper and lower tolerances around expected line.
phase	Character string. Specify which phase to examine for deviations (usually this is "coupling" phase).

Value

A vector of deviations in LOD scores outside the range defined by tolerances input alpha

Examples

data("SN_SN_P1")
SNSN_LOD_deviations(SN_SN_P1,4,198)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.