QQ plot
On 12/11/2019 2:56 p.m., Jim Lemon wrote:
I thought about this and did a little study of GWAS and the use of p-values to assess significant associations. As Ana's plot begins at values of about 0.001, this seems to imply that almost everything in the genome is associated to some degree. One expects that most SNPs will not be associated with a particular condition (p~1), so perhaps something is going wrong in the calculations that produce the p-values.
I may be misunderstanding your last sentence, but if there is no
association, the p-value would usually have a uniform distribution from
0 to 1, it wouldn't be near 1.
I'd guess we're not seeing the p values from every test, only those that
are less than 0.001. If that's true, and there are no effects, it makes
sense to multiply all of them by 1000 to get U(0,1) values. On the
plot, that would correspond to subtracting 3 from -log10(p), or adding 3
to the reference line, as Ana requested.
Or just multiply them by 1000 and pass them to qq():
qq(dd$P*1000, main = "Q-Q plot of small GWAS p-values")
As far as I can see, there's no way to tell qqman::qq to move the
reference line.
Duncan Murdoch
Jim On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) <malone at malonequantitative.com> wrote:
I agree with Abby. That would defeat the purpose of a QQ plot. On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdle.a at gmail.com> wrote:
Hi I'm not familiar with the qqman package, or GWAS studies. However, my guess would be that you're *not* supposed to change the position of the line. On Tue, Nov 12, 2019 at 11:48 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
Hi, I was using this library, qqman https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html to create QQ plot, attached. How would I change this default abline to start from the beginning of my QQ line? This is my code: qq(dd$P, main = "Q-Q plot of GWAS p-values") Thanks Ana
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