Prepare and run mediation for a set of QTL peaks

Usage

modiFinder(
  peaks,
  mapping,
  sigLOD = 7.5,
  annots,
  outdir = NULL,
  med_out = "mediation.rds",
  total_cores = NULL,
  save = "sr",
  distOnly = TRUE,
  hsOnly = FALSE
)

Arguments

peaks: List of dataframes containing QTL peaks for each tissue, or full path to .rds containing one.
mapping: Mapping list from mapQTL, or full path to .rds containing one.
sigLOD: Significant LOD threshold to use to filter phenotypes for mediation. Default is 7.5
annots: Annotations file. Contains mapping information for phenotypes. Dataframe, or tsv. Columns must include "id", "symbol", "start", "end".
outdir: Directory to save output files. Default is NULL.
med_out: String indicating the name of the output file containing mediation results for mediation within a phenotype. This file will be saved in .rds format and used for downstream analysis and visualization. Should end in .rds. Default is "mediation.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".
distOnly: Logical. Mediate only the distal peaks? Default is TRUE.
hsOnly: Logical. Mediate only on peaks identified within a hotspot. Default is FALSE.

Value

A list containing mediation results for each tissue