Prepare and run between phenotype mediation for a set of QTL peaks with provided expression data.

Mediation scan between two different phenotypes. Provide peaks and mapping for the phenotype to mediate, and the rank Z-transformed phenotype quantification to use as mediators.

Usage

multi_modiFinder(
  peaks,
  mapping,
  exprZ,
  suggLOD = 7,
  annots,
  outdir = NULL,
  med_out = "multi_pheno_mediation.rds",
  total_cores = NULL,
  save = "sr"
)

Arguments

peaks: List of dataframes containing QTL peaks for each tissue, or full path pointing to saved peaks object.
mapping: Mapping list from mapQTL, or full path to .rds containing one.
exprZ: rankZ transformed expression to use for the mediation.
suggLOD: 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 between phenotypes. This file will be saved in .rds format and used for downstream analysis and visualization. Should end in .rds. Default is "multi_pheno_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".

Value

A list containing mediation results for each tissue