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

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

# \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)
# }