annotate_lods: Annotate LOD peaks with variance explained, effect size, and...

In AndersenLab/linkagemapping: Functions for the Mapping of Andersen Lab RIAILs and RILs

Description

Annotate LOD peaks with variance explained, effect size, and confidence interval bounds

Usage

annotate_lods(
  lods,
  cross,
  annotate_all = FALSE,
  bayes = FALSE,
  cutoff = "chromosomal"
)

Arguments

lods	A data frame output by the mapping functions to be converted to a scanone object
cross	The cross object used for the original mapping
annotate_all	Boolean whether or not to annotate all markers with variance explained and effect size. If FALSE (default), only peak lods will be annotated.
bayes	Boolean whether or not to calculate confidence intervals based on Bayes statistics (LOD drop 1.5 used to find CI by default)
cutoff	Determines strategy for setting CI (not available for Bayes CIs). Either "chromosomal" (default), including leftmost and rightmost markers across peak chromosome with LOD above cutoff or "proximal" that ends the CI at the most proximal left and right marker that drop below cutoff.

Value

The annotated lods data frame with information added for peak markers of each iteration

AndersenLab/linkagemapping documentation built on Jan. 27, 2022, 10:44 p.m.