manhattan3: Draw the effects of epistasis (3d plot and 2d plot)

In KosukeHamazaki/RAINBOW: Genome-Wide Association Study with SNP-Set Methods

Description

Draw the effects of epistasis (3d plot and 2d plot)

Usage

manhattan3(
  input,
  cum.pos,
  plot.epi.3d = TRUE,
  plot.epi.2d = TRUE,
  main.epi.3d = NULL,
  main.epi.2d = NULL,
  saveName = NULL
)

Arguments

input	Data frame of GWAS results where the first column is the marker names, the second and third column is the chromosome amd map position, and the forth column is -log10(p) for each marker.
cum.pos	Cumulative position (over chromosomes) of each marker
plot.epi.3d	If TRUE, draw 3d plot
plot.epi.2d	If TRUE, draw 2d plot
main.epi.3d	The title of 3d plot. If this argument is NULL, trait name is set as the title.
main.epi.2d	The title of 2d plot. If this argument is NULL, trait name is set as the title.
saveName	When drawing any plot, you can save plots in png format. In saveName, you should substitute the name you want to save. When saveAt = NULL, the plot is not saved.

Value

Draw 3d plot and 2d plot to show epistatic effects

KosukeHamazaki/RAINBOW documentation built on Dec. 12, 2020, 8:35 p.m.