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

In dingruofan/xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

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,
  axis_text_size = 1.3,
  axis_title_size = 1.3,
  title_size = 1.4,
  title_text = "",
  point_color = "#5A90BE"
)

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.
axis_text_size	(numberic) text size of the axis labels
axis_title_size	(numberic) text size of the axis title
title_size	(numberic) text size of the title of the plot
title_text	(character) title of the plot
point_color	(character) Color of the point, default: #5A90BE

Value

ggplot2 object

Examples

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)

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.