fastman: fastman

In danioreo/fastman: A Fast Way to Create Manhattan Plots for GWAS Data

fastman

Description

Creates Manhattan plots from GWAS summaries.

Usage

fastman(data, chr = "CHR", ps = "BP", p = "P", main = "Manhattan plot",
  suggest_line = -log10(1e-05), gws_line = -log10(5e-08),
  color = c("grey", "black"), chr_build = "GRCh37", yscale = NA,
  xlab_all = F, turbo = F)

Arguments

data	A GWAS summary with columns of chromosome number (X and Y chromosomes need to be replaced by 23 and 24), position (base pair) information, and P-value. ALL values have to be numeric.
chr	A string for the header of the column of chromosome number in data.
ps	A string for the header of the column of position (base pair) information in data.
p	A string for the header for the column of P-value in data.
main	A string for the Title of the plot.
suggest_line	Set FALSE to remove the suggestive threshold line.
gws_line	Set FALSE to remove the genome-wide significant line.
color	A string vector containg the colors to be used.
chr_build	A string describing what Genetic Reference Consortium build is used. It has to be either "GRCh37" or "CRCh38".
yscale	A numeric value for y scale.
xlab_all	Set TRUE to show labels for all chromosomes.
turbo	Set TRUE to remove all rows with P <= 0.1.

danioreo/fastman documentation built on July 28, 2022, 9 p.m.