[R] QQ plot

[Ana Marija]

Hi Duncan,

yes I choose for QQ plot only P<1e-3 and multiplying everything with
1000 works great!
This should not in my understanding influence the interpretation of
the plot, it is only changing the scale of axis.

Thank you so much,
Ana

On Tue, Nov 12, 2019 at 2:51 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> 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$P*1000, main = "Q-Q plot of small GWAS p-values")
>
> As far as I can see, there's no way to tell qqman::qq to move the
> reference line.
>
> Duncan Murdoch
>
> >
> > Jim
> >
> > On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative)
> > <malone using malonequantitative.com> wrote:
> >>
> >> I agree with Abby. That would defeat the purpose of a QQ plot.
> >>
> >> On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdle.a using gmail.com> wrote:
> >>
> >>> Hi
> >>>
> >>> I'm not familiar with the qqman package, or GWAS studies.
> >>> However, my guess would be that you're *not* supposed to change the
> >>> position of the line.
> >>>
> >>> On Tue, Nov 12, 2019 at 11:48 AM Ana Marija <sokovic.anamarija using gmail.com>
> >>> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I was using this library, qqman
> >>>> https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html
> >>>>
> >>>> to create QQ plot, attached. How would I change this default abline to
> >>>> start from the beginning of my QQ line?
> >>>>
> >>>> This is my code:
> >>>> qq(dd$P, main = "Q-Q plot of GWAS p-values")
> >>>>
> >>>> Thanks
> >>>> Ana
> >>>> ______________________________________________
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> >>
> >>          [[alternative HTML version deleted]]
> >>
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> ______________________________________________
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