xQTLbiolinks (version 1.6.2)

xQTLvisual_manhattan: Manhattan plot for a GWAS summary statistics dataset

Description

Manhattan plot for a GWAS summary statistics dataset

Usage

xQTLvisual_manhattan(gwasDF, pvalue_cutoff = 1e-04, num_snp_selected = 2000)

Value

A pdf format figure.

Arguments

gwasDF

A data.frame of summary statistics data, including four cols arranged in the following order: SNP name, chomosome, position, p-value.

pvalue_cutoff

Default: 1e-4. The Manhattan plot is a helpful tool for visualizing genome-wide association study results. However, when there are a large number of SNPs, the plot can become difficult to render and generate a large file size. This is due to the stacking of non-significant SNPs at the bottom of the plot. To address this issue, we can choose to filter out some of the non-significant SNPs or randomly select a subset of them to plot. This will improve the readability of the plot and reduce the file size.

num_snp_selected

Default: 2000. Number of SNPs randomly selected for each chromosome.

Examples

# \donttest{
gwasDF <- data.table::fread(
      "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/AD/gwasChr6Sub.txt")
xQTLvisual_manhattan(gwasDF[,.(rsid, chr, position,P)])
# }