[R] QQ plot

[Bert Gunter]

Typo: "... from 5.5 million..."

Bert


On Tue, Nov 12, 2019 at 3:11 PM Bert Gunter <bgunter.4567 using gmail.com> wrote:

> 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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