[R] QQ plot

[Ana Marija]

Just do I need to change the axis when I multiply with 1000 and what
should I put on my axis?

On Tue, Nov 12, 2019 at 3:07 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> 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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> > >>>
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> > >>>
> > >>
> > >>          [[alternative HTML version deleted]]
> > >>
> > >> ______________________________________________
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> > >
> > > ______________________________________________
> > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> > >
> >
> > ______________________________________________
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> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.