Identify distal hotspots above a suggestive and significant LOD score.

Identify distal hotspots above a suggestive and significant LOD score.

Usage

transbands(
  map_dat,
  peaks,
  sigLOD = 7.5,
  suggLOD = 6,
  psave = TRUE,
  pname = NULL,
  outdir = NULL,
  color = "#0073C2FF"
)

Arguments

map_dat

map_dat2 from mapQTL mapping list.

peaks

List of dataframes containing QTL peaks for each tissue (annotated).

sigLOD

Significant LOD threshold to use for filtering phenotypes. Default is 7.5

suggLOD

Suggestive LOD threshold to use for filtering phenotypes. Default is 6.

psave

Logical. Save the plot as .png. Default TRUE.

pname

File name to save plot (needs to end in .png). Default is hotspots_<tissue>.png

outdir

Directory to save plots. Default is NULL.

color

Plot color. Default is "#0073C2FF".

Value

A list containing:

• bands.rnaA list of tibbles containing hotspot information for each tissue Information includes the following for each hotspot:

  • Chromosome of the hotspot

  • Start and Stop (bp) of the hotspot

  • The number of significant peaks within the hotspot

  • The number of suggestive peaks within the hotspot

  trans_band_plotsA list of ggplot2 objects (one for each tissue), showing the number of significant distal hotspot peaks.