xQTLvisual_PZPlot: Compare P-values reported to P-values calculated from Z...
In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
xQTLvisual_PZPlot R Documentation
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"
)
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"
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")
xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.
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| xQTLvisual_PZPlot | R Documentation |
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"
)
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" |
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")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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