Calculate founder effects for significant peaks

Usage

qtl_effects(
  peaks,
  mapping,
  suggLOD = 6,
  outdir = NULL,
  effects_out = "effects.rds",
  total_cores = NULL,
  save = "sr"
)

peaks: List of dataframes containing annotated QTL peaks for each tissue, or full path to .rds containing one.
mapping: Mapping list from mapQTL, or full path to .rds containing one.
suggLOD: Suggestive LOD threshold to use for filtering phenotypes. Default is 6.
outdir: Directory to save effects output files. Default is NULL.
effects_out: String indicating the name of the output file containing founder haplotype effects results. This file will be saved in .rds format and used for downstream analysis and visualization. Should end in .rds. Default is "effects.rds"
total_cores: Number of available cores to use for parallelization. Default is NULL.
save: Indicates object return/save behavior. One of c("sr", "so", "ro"); save & return, save only, return only. Default is "sr".

A list containing:

effects_blupQTL effect BLUPs from scan along one chromosome. Output from qtl2::scan1blup()
peaksannotated peaks with LOD scores above suggestive threshold