Identify top mediators within a hotspot (molecular QTL)

Usage

medPlot_hotSpot(
  peaks,
  meds,
  tbands,
  chromosome,
  sigLOD,
  hsNum = 1,
  top_n = 5,
  plot = "padj",
  topFeats = NULL,
  psave = TRUE,
  pname = NULL,
  outdir = NULL,
  showTarg = T
)

Arguments

peaks: Dataframe of peaks to pull targets from (output of mapQTL, then select peaks_list$tissue).
meds: Dataframe of mediation to pull potential mediators from (output from modiFinder, then select $tissue).
tbands: Dataframe of all transbands (output of transbands, then select bands.rna$tissue).
chromosome: Chromosome that the transband (hotspot) is present on.
sigLOD: Significant LOD threshold to use for filtering phenotypes.
hsNum: If there are multiple hotspots on a chromosome, indicate which one. Default is 1.
top_n: The number of top mediators per target to show, determined by LOD drop. Default is 5. NB If you want to see all the mediators, set this to the number of mediators in your hotspot.
plot: One of c("padj", "pval", "per_drop", "ranks") depending on what statistic should be plotted in the heatmap. Default "padj".
topFeats: Optional. Top hotspot features based on PC analysis.
psave: Logical. Save the plot as .png. Default TRUE.
pname: String indicating the name of plot to save as a .png. Default "mediation_plot_chrtop<top_n>.png".
outdir: Directory to save plots. Default is NULL.
showTarg: Logical. Show target names in resulting plot. Default TRUE.

Value

A list containing a dataframe representing the ranking of each mediator within the hotspot for each target of the hotspot and the heatmap object.