manhattan: A "manhattan" plot for genome-wide genetic association...

In kenhanscombe/associatr: Genetic Association Plots

Description

A scatter plot of negative log base 10 p-value against genomic position

Usage

manhattan(
  data,
  trait_label = "phenotype",
  trim = 0.001,
  chromosome = "#CHROM",
  snp = "SNP",
  bp = "POS",
  a1 = "A1",
  effect = "BETA",
  p = "P",
  chr_color = c("#878D92", "#49494D"),
  strip_color = "grey25",
  ...
)

Arguments

data	A genetic association results dataframe.
trait_label	A character vector to be used as label. Default = "phenotype".
trim	Observations with p-values larger than the trim value are dropped. Default = 0.001.
chromosome	An integer vector of chromosome codes.
snp	SNP id.
bp	Base-pair coordinate.
a1	Allele 1 (usually minor). See details.
effect	Regression coefficient or odds ratio.
p	Association p-value.
chr_color	A character vector of 2 colours to be used on alternate chromosomes.
strip_color	Color of the vertical strip describing the panel.
...	Additional arguments passed to geom_point.

Details

SNP id (snp), Allele 1 (a1), and regression coefficient or odds ratio (effect) columns are only used for labelling points. a1 is described as it is in PLINK documentation, but as this column is only used for labelling it can refer to any allele. PLINK output names are used as the default values for all columns.

kenhanscombe/associatr documentation built on Nov. 13, 2020, 9:24 a.m.