Wrapper function to generate mapping, peaks, mediation, and effects data

Usage

runQTL(
  geno_out = "gbrs_interpolated_genoprobs.rds",
  peaks_out = "peaks.rds",
  map_out = "mapping.rds",
  med_out = "mediation_res.rds",
  effects_out = "effects.rds",
  outdir = NULL,
  gbrs_fileLoc,
  metadata,
  expr_mats,
  covar_factors,
  annots,
  tissues = c(),
  gridFile = gridfile,
  total_cores = NULL,
  save_t = "sr",
  ...
)

Arguments

geno_out: String indicating the name of the output file containing interpolated genotype probabilities. This file will be saved in .rds format and used for QTL mapping. Should end in .rds. Default is "gbrs_interpolated_genoprobs.rds".
peaks_out: String indicating the name for output peaks file. This file will be saved in .rds format and will be used as an input for downstream analysis. Should end in .rds. Default is "peaks.rds"
map_out: String indicating the name of the output file containing QTL mapping results. This file will be saved in .rds format and will be used in downstream analyses. Should end in .rds. Default is "map.rds"
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"
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"
outdir: Directory to save output files. Default is NULL.
gbrs_fileLoc: Path to GBRS interpolated tsv files.
metadata: Sample metadata. Either a string pointing to the file, or the object itself.
expr_mats: List of normalized count matrices (objects), or character paths to the file. One matrix per tissue. The order must match the tissue order in genoprobs.
covar_factors: Additive covariate factors. These need to be columns in the sample metadata.
annots: Annotations file. Contains mapping information for phenotypes. Dataframe, or tsv. Columns must include "id", "symbol", "start", "end".
tissues: Vector of strings indicating tissues or conditions in project.
gridFile: Genome Grid. Path to location or object. Defaults to 75k grid loaded with package.
total_cores: Number of available cores to use for parallelization. Default is NULL.
save_t: Indicates object return/save behavior. One of c("sr", "so", "ro"); save & return, save only, return only. Default is "sr".

Value

A list containing

peaks_listUnfiltered peaks for each tissue.
maps_listList of objects associated with mapping. See mapQTL help for details.
res_listList containing mediation results for each tissue.
effects_resList of objects associated with effects. See qtl_effects help for details.