[R] QQ plot

[Ana Marija]

Hi Michael,

Thank you so much for that valuable idea!
I will try first to clump or remove SNPs in LD and maybe the situation
would improve.
But this procedure of yours is definitely something that would come
handy in future!

Cheers,
Ana

On Wed, Nov 13, 2019 at 5:47 AM Michael Dewey <lists using dewey.myzen.co.uk> wrote:
>
> Dear Ana
>
> As others have commented this is getting a bit off-topic but here are
> some hints.
>
> It is helpful to distinguish  two sorts of plot: archival plots and
> impact plots. If you want to have an impact plot which gives you a
> picture but possibly at the cost of completeness and accuracy then why not:
>
> 1 - plot a sample of your 5 million drawn at random
> 2 - bin the data and plot median p-value against median expected
> 3 - deal with overlap by choosing a graphical device which supports
> transparency and plot points in very light grey so the overlap is more
> visible.
>
> Michael
>
> On 12/11/2019 22:04, Ana Marija 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.
> >>>>>>>>
> >>>>>>>> ______________________________________________
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> >>>>>>>>
> >>>>>>>
> >>>>>>>           [[alternative HTML version deleted]]
> >>>>>>>
> >>>>>>> ______________________________________________
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> >>>>>>
> >>>>>> ______________________________________________
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> >>>>>>
> >>>>>
> >>>>> ______________________________________________
> >>>>> 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.
> >
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html