manhattan.plus: Add points of -log10(p) corrected by kernel methods to...

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

Add points of -log10(p) corrected by kernel methods to manhattan plot

Description

Add points of -log10(p) corrected by kernel methods to manhattan plot

Usage

manhattan.plus(
  input,
  checks,
  cex = 1,
  plot.col1 = c("dark blue", "cornflowerblue"),
  plot.col3 = c("red3", "orange3"),
  plot.type = "p",
  plot.pch = 16
)

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.
checks	The marker numbers whose -log10(p)s are corrected by kernel methods.
cex	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
plot.col1	This argument determines the color of the manhattan plot. You should substitute this argument as a color vector whose length is 2. plot.col1[1] for odd chromosomes and plot.col1[2] for even chromosomes.
plot.col3	Color of -log10(p) corrected by kernel methods. plot.col3[1] for odd chromosomes and plot.col3[2] for even chromosomes
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".

Value

Draw manhttan plot

RAINBOWR documentation built on Sept. 12, 2023, 9:08 a.m.