[R] QQ plot

Wed Nov 13 00:11:46 CET 2019

IMO, this thread has now gone totally off the rails and totally off topic
-- it is clearly *not* about R programming and totally about statistics.

I believe Ana Marija would do better to get local statistical help or post
on a statistics or genomics list (stats.stackexchange.com is one such)
where she can engage in a fuller discussion of what an *appropriate* qqplot
would tell her. Of course selecting the lowest 3700 p-values from 55.5
million and plotting them against 3700 expected uniform quantiles will not
give a line with 0 intercept and slope 1. The scale correction is easy to
make, but it is not multiplying by 1000!

Bert

On Tue, Nov 12, 2019 at 2:11 PM Ana Marija <sokovic.anamarija using gmail.com>
wrote:

> why I selected only those with P<0.003 to put on QQ plot is because
> the original data set contains 5556249 points and when I extract only
> P<0.001 I am getting 3713 points. Is there is a way to plot the whole
> data set, or choose only the representative points?
>
> On Tue, Nov 12, 2019 at 3:42 PM Ana Marija <sokovic.anamarija using gmail.com>
> wrote:
> >
> > the smallest p value in my dataset goes to 9.89e-08. How do I make
> > that known on the new QQ plot with multiplied with 1000 values
> >
> > On Tue, Nov 12, 2019 at 3:37 PM Ana Marija <sokovic.anamarija using gmail.com>
> wrote:
> > >
> > > 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
> > > > > >>>> ______________________________________________
> > > > > >>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and
> more, see
> > > > > >>>> https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > >>>> PLEASE do read the posting guide
> > > > > >>> http://www.R-project.org/posting-guide.html
> > > > > >>>> and provide commented, minimal, self-contained, reproducible
> code.
> > > > > >>>
> > > > > >>> ______________________________________________
> > > > > >>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more,
> see
> > > > > >>> https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > >>> PLEASE do read the posting guide
> > > > > >>> http://www.R-project.org/posting-guide.html
> > > > > >>> and provide commented, minimal, self-contained, reproducible
> code.
> > > > > >>>
> > > > > >>
> > > > > >>          [[alternative HTML version deleted]]
> > > > > >>
> > > > > >> ______________________________________________
> > > > > >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more,
> see
> > > > > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > > > > >> and provide commented, minimal, self-contained, reproducible
> code.
> > > > > >
> > > > > > ______________________________________________
> > > > > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more,
> see
> > > > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > > > > > and provide commented, minimal, self-contained, reproducible
> code.
> > > > > >
> > > > >
> > > > > ______________________________________________
> > > > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > > > > and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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