[R] data load from excel files

Dear R-Help, I have 30 of year-based excel files and each file contain month sheets. I have some problem here. My data is daily rainfall but there is extra 1 day (first date of next month) for several sheets. My main goal is to get the minimum value for every month. First, how to extract those da

Re: [R] QQ plot

Typo: "... from 5.5 million..." Bert On Tue, Nov 12, 2019 at 3:11 PM Bert Gunter 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 s

Re: [R] QQ plot

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

Re: [R] QQ plot

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 Ma

Re: [R] QQ plot

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 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 1

Re: [R] QQ plot

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 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 influen

Re: [R] QQ plot

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 wrote: > >

Re: [R] QQ plot

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 expec

Re: [R] QQ plot

That refers to "normally" distributed data (see Greg Snow's comment below the one you cite). P-values are not necessarily normally distributed as you can see, and they must have a non-zero mean. Jim On Wed, Nov 13, 2019 at 7:07 AM Ana Marija wrote: > > Hi, > > what I know so far that this kind o

Re: [R] QQ plot

As this is O/T I'll keep it offlist. Inline: On Tue, Nov 12, 2019 at 12:00 PM 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 ev

Re: [R] QQ plot

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 P

Re: [R] QQ plot

Just a small comment. In GWAS studies p values are considerate to bi significant whwn p < 10-6 or smaller regards, Miloš On Tue, 12 Nov 2019 at 21:00, 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 pl

Re: [R] QQ plot

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 wrote: > > Hi, > > what I know so far that this kind of

Re: [R] using xpath with xml2

Forehead smack! Of course! Thank you, Bill! > On Nov 12, 2019, at 2:50 PM, William Dunlap wrote: > > > xml_ns(daymet) > d1<-> http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0 > > xlink <-> http://www.w3.org/199

Re: [R] QQ plot

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 wit

Re: [R] using xpath with xml2

> xml_ns(daymet) d1<-> http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0 xlink <-> http://www.w3.org/1999/xlink > daymet %>% xml2::xml_find_all(xpath = "d1:dataset") {xml_nodeset (1)} [1] https://thredds.daac.ornl.gov/thredds/catalog/ornldaac/1328/catalog.xml"; > > # run the follo

[R] using xpath with xml2

Hi, I have mined XML extensively with R before now, but my xpath chops seem to be regressing recently. I know that I can roll up my sleeves and search through the child nodes of the root, but I can't noodle out why using the xpath description returns an empty nodeset. Any suggestions and nudge

Re: [R] QQ plot

I agree with Abby. That would defeat the purpose of a QQ plot. On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle 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, 20