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

In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

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

Description

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

Usage

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

Arguments

input	List of results of RGWAS.epistasis / RGWAS.twostep.epi. If the output of 'RGWAS.epistasis' is 'res', 'input' corresponds to 'res$scores'. If the output of 'RGWAS.twostep.epi.' is 'res', 'input' corresponds to 'res$epistasis$scores'. See: Value of RGWAS.epistasis
map	Data frame with the marker names in the first column. The second and third columns contain the chromosome and map position. This is map information for SNPs which are tested epistatic effects.
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

RAINBOWR documentation built on July 4, 2024, 1:11 a.m.