[R] QQ plot

[Jim Lemon]

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.

Jim

On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative)
<malone using 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 using 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 using 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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> >
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