[R] QQ plot

Ana Marija @okov|c@@n@m@r|j@ @end|ng |rom gm@||@com
Tue Nov 12 21:15:58 CET 2019


details about my data if it is helpful:

> median(dd$P,na.rm = FALSE)
[1] 0.000444
> mean(dd$P,na.rm = FALSE)
[1] 0.000461
> min(dd$P,na.rm = FALSE)
[1] 9.89e-08
> max(dd$P,na.rm = FALSE)
[1] 0.001

On Tue, Nov 12, 2019 at 2:07 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hi,
>
> what I know so far that this kind of QQ plot is an indication that
> data has non zero mean:
> https://stats.stackexchange.com/questions/280634/how-to-interpret-qq-plot-not-on-the-line
>
> but is that an indication that something is wrong with the analysis?
>
> Thanks
> Ana
>
> On Tue, Nov 12, 2019 at 2:00 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.
> >
> > 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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> > >
> > >         [[alternative HTML version deleted]]
> > >
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> > > and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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