xQTLbiolinks (version 1.6.2)

xQTLvisual_qqPlot: Quantile-quantile plot with p-values from GWAS summary statistics data

Description

Quantile-quantile plot with p-values from GWAS summary statistics data

Usage

xQTLvisual_qqPlot(
  summaryDT,
  legend_p = FALSE,
  binCutLogP = 3,
  binNumber = 1000
)

Value

ggplot2 object

Arguments

summaryDT

A data.frame of one col required: pval.

legend_p

TRUE or FALSE, or legend position, including: top, bottom, left and right.

binCutLogP

SNPs whose logP great than this will be binned, other than not binned.

binNumber

Number of bins.

Examples

# \donttest{
url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/gwasSub.txt.gz"
snpInfo <- data.table::fread(url1, sep="\t")
xQTLvisual_qqPlot(snpInfo[,.(pValue)],binCutLogP=5, binNumber=10000)
# }