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.anamar...@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.anamar...@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.anamar...@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.anamar...@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.dun...@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$P*1000, main = "Q-Q plot of small GWAS p-values") > > > > > > > > > > As far as I can see, there's no way to tell qqman::qq to move the > > > > > reference line. > > > > > > > > > > Duncan Murdoch > > > > > > > > > > > > > > > > > Jim > > > > > > > > > > > > On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) > > > > > > <mal...@malonequantitative.com> wrote: > > > > > >> > > > > > >> I agree with Abby. That would defeat the purpose of a QQ plot. > > > > > >> > > > > > >> On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdl...@gmail.com> > wrote: > > > > > >> > > > > > >>> Hi > > > > > >>> > > > > > >>> I'm not familiar with the qqman package, or GWAS studies. > > > > > >>> However, my guess would be that you're *not* supposed to > change the > > > > > >>> position of the line. > > > > > >>> > > > > > >>> On Tue, Nov 12, 2019 at 11:48 AM Ana Marija < > sokovic.anamar...@gmail.com> > > > > > >>> wrote: > > > > > >>>> > > > > > >>>> Hi, > > > > > >>>> > > > > > >>>> I was using this library, qqman > > > > > >>>> > https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html > > > > > >>>> > > > > > >>>> to create QQ plot, attached. How would I change this default > abline to > > > > > >>>> start from the beginning of my QQ line? > > > > > >>>> > > > > > >>>> This is my code: > > > > > >>>> qq(dd$P, main = "Q-Q plot of GWAS p-values") > > > > > >>>> > > > > > >>>> Thanks > > > > > >>>> Ana > > > > > >>>> ______________________________________________ > > > > > >>>> R-help@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@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@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@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@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@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@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.
