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

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

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

# \donttest{
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")
# }