HodgesTools (version 1.0.0)

createManhattandQQ: Creating a Manhattan Plot and QQ plot

Description

Creates a Manhattan plot and QQ plot using GWAS results output from PLINK

Usage

createManhattandQQ(
  gwas_results,
  highlights_file = NULL,
  suggestive_line = -log10(0.05),
  set_color_vector = c("gray10", "gray60"),
  genomewide_line = -log10(5e-08),
  annotate_Pval = 0.05,
  y_lim = c(0, 8)
)

Value

a Manhattan plot of SNP-trait associations and QQ plot

Arguments

gwas_results

output file listing SNP-trait association values for GWAS run using PLINK

highlights_file

a text file with a 'snp' column listing the SNPs to annotate/color on the Manhattan plot

suggestive_line

where to draw a "suggestive" line; default -log10(1e-5).

set_color_vector

a character vector listing colors in palette of interest (you must create this chr object before calling the createManhattanandQQ function and assign it to set_color_vector)

genomewide_line

where to draw a "genome-wide significant" line; default -log10(5e-8)

annotate_Pval

if set, SNPs below this p-value will be annotated on the plot; default is 0.05

y_lim

set the y-axis limits; default is c(0,8)

Author

Verda Agan

Details

This function reads in a GWAS result file output from plink2 listing the coordinates, ids, and associated p-values for SNPs under study This function also has the option of reading in a "highlights" file listing the IDs of SNPs to annotate/color on the Manhattan plot

Examples

#' #load external data.
gwas_results <- system.file(package = "HodgesTools", "extdata",
"createManhattandQQ_example_sum_stats.txt")
snps_to_annotate <- system.file(package = "HodgesTools", "extdata",
"createManhattandQQ_example_highlights_file.txt")

#Make a Manhattan plot that highlights a select list of SNPs subset from GWAS results
createManhattandQQ(gwas_results, highlights_file=snps_to_annotate,
suggestive_line = -log10(0.001), set_color_vector = c("gray10", "gray60"),
genomewide_line = -log10(5e-8), annotate_Pval = 0.001, y_lim =c(0,8))

#Make a Manhattan plot that doesn't highlight a select list of SNPs subset from GWAS results
createManhattandQQ(gwas_results, suggestive_line = -log10(0.001),
set_color_vector = c("gray10", "gray60"), genomewide_line = -log10(5e-8),
annotate_Pval = 0.001, y_lim =c(0,8))