effectplot: Plot effect size by marker

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

Description

Plot effect size by marker

Usage

effectplot(
  cross,
  map,
  parental = "N2xCB4856",
  bayes_param = F,
  cutoff_param = "chromosomal",
  tsize = 20
)

Arguments

cross	The cross object used for the mapping (output of mergepheno() function)
map	The mapping output for a single trait
parental	The parental strains used to generate RIAILs. Either "N2xCB4856" (default), "N2xLSJ2", or "AF16xHK104
bayes_param	Boolean whether or not to calculate confidence intervals based on Bayes statistics (LOD drop 1.5 used to find CI by default). Default is FALSE
cutoff_param	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.
tsize	The theme size of the text for the plot, default is 20

Value

A line plot of the effect size at each marker

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