xQTLvisual_PZPlot: Compare P-values reported to P-values calculated from Z...

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

Compare P-values reported to P-values calculated from Z statistics derived from the reported beta and standard error.

Description

Compare P-values reported to P-values calculated from Z statistics derived from the reported beta and standard error.

Usage

xQTLvisual_PZPlot(
  summaryDT,
  binCutLogP = 4,
  binNumber = 2000,
  distribution_func = "pnorm",
  axis_text_size = 1.3,
  axis_title_size = 1.3,
  title_size = 1.4,
  title_text = "",
  point_color = "#5A90BE"
)

Arguments

summaryDT	A data.frame with three cols: pval, beta, se.
binCutLogP	To speed up the rendering process of the plot for tens of millions of GWAS variants, variants with a p-value below a specified threshold (binCutLogP) are randomly sampled for display.
binNumber	The number of points randomly selected for plotting.
distribution_func	"pnorm"(default) or "pchisq"
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

Value

a list containing a data.frame of estimated pvalues and A ggplot2 object

Examples

url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwasDFsub_MMP7.txt"
sumDT <- data.table::fread(url1, sep="\t")
xQTLvisual_PZPlot(sumDT[,.(pValue, beta, se)], distribution_func="pchisq")

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