Question: Q-Q plots with GWAS p-values using R (needs confidence band)

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joshf •

**20**wrote:I'm trying to create Q-Q plots with GWAS p-values using **R** but it hasn't really been working out. I need for them to be on a -log10 scale, and for them to have a confidence band/interval.

I tried out:

**qqman**- works great and it's simple but it does not provide a confidence interval function> code:`qq(*P-values*)`

**snpStats**- has the confidence interval but the X and Y axis are chi-squared values. I'm not sure if there's a way to get -log10 P-values? The plots look great though. code:`qq.chisq(-2 * log(*P-values*), df = 2, pvals= TRUE, conc=c(0.05, 0.95))`

**car -**the plot looks a little....odd. Maybe I'm just using it wrong but I don't like the distribution of the dots. Why does the X-axis start at -4 instead of 0? code:`qqPlot(-log10(*P-values*), envelope=0.95)`

I'm hoping the colorful examples would help me get a detailed answer lol

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modified 22 months ago
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Kevin Blighe ♦

**61k**• written 4.4 years ago by joshf •**20**