polymapR (version 1.1.1)

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

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

# NOT RUN {
data("SN_SN_P1")
SNSN_LOD_deviations(SN_SN_P1,ploidy = 4, N = 198)
# }