[R] QQ plot

[Bert Gunter]

As this is O/T I'll keep it offlist.

Inline:


On Tue, Nov 12, 2019 at 12:00 PM Jim Lemon <drjimlemon using gmail.com> 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.
>

Exactly! Or possibly with the data handling pipeline prior to getting into
R.

-- Bert



>
> 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.
>

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