manhattan2: Draw manhattan plot (another method)

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

Draw manhattan plot (another method)

Description

Draw manhattan plot (another method)

Usage

manhattan2(
  input,
  sig.level = 0.05,
  method.thres = "BH",
  cex = 1,
  plot.col2 = 1,
  plot.type = "p",
  plot.pch = 16,
  cum.pos = NULL,
  lwd.thres = 1,
  cex.lab = 1,
  cex.axis = 1
)

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.
sig.level	Siginifincance level for the threshold. The default is 0.05.
method.thres	Method for detemining threshold of significance. "BH" and "Bonferroni are offered.
cex	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
plot.col2	Color of the manhattan plot. color changes with chromosome and it starts from plot.col2 + 1 (so plot.col2 = 1 means color starts from red.)
plot.type	This argument determines the type of the manhattan plot. See the help page of "plot".
plot.pch	This argument determines the shape of the dot of the manhattan plot. See the help page of "plot".
cum.pos	Cumulative position (over chromosomes) of each marker
lwd.thres	The line width for the threshold.
cex.lab	The font size of the labels.
cex.axis	The font size of the axes.

Value

Draw manhttan plot

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