Hi Jim, not in this case, but thanks for asking!
Ana On Mon, Jun 1, 2020 at 10:04 PM Jim Lemon <[email protected]> wrote: > > So recombination sticks out its foot before us. Do you want to account > for gene linkage? > > JIm > > On Tue, Jun 2, 2020 at 11:55 AM Ana Marija <[email protected]> > wrote: > > > > Hi Jim > > > > > neu3<-neu1[!(neu1$Marker %in% Marker3),] > > > dim(neu3) > > [1] 1857 9 > > > nep3<-nep1[!(nep1$Marker %in% Marker3),] > > > dim(nep3) > > [1] 5562 9 > > > ret3<-ret1[!(ret1$Marker %in% Marker3),] > > > dim(ret3) > > [1] 3493 9 > > > > > > If I do: > > > > nn1<-merge(neu1,nep1,by=c("Marker","Chr")) > > nn2<-merge(nn1,ret1,by=c("Marker","Chr")) > > > Marker3<-nn2$Marker > > > length(Marker3) > > [1] 3742962 > > > Marker4<-nn1$Marker > > > length(Marker4) > > [1] 3744443 > > > > On Mon, Jun 1, 2020 at 8:50 PM Ana Marija <[email protected]> > > wrote: > > > > > > Hi David, > > > > > > that is a great point! > > > Yes indeed some are non unique: > > > > > > > dim(neu1) > > > [1] 3742845 9 > > > > length(unique(neu1$Marker)) > > > [1] 3741858 > > > > length(unique(nep1$Marker)) > > > [1] 3745560 > > > > dim(nep1) > > > [1] 3746550 9 > > > > length(unique(ret1$Marker)) > > > [1] 3743494 > > > > dim(ret1) > > > [1] 3743494 9 > > > > > > How would I rewrite this code so that is merging by Chr and Marker > > > column? It seems that a Marker can be under a few Chr. > > > > > > > > > > > > > > > > > > On Mon, Jun 1, 2020 at 8:41 PM David Winsemius <[email protected]> > > > wrote: > > > > > > > > > > > > On 6/1/20 5:40 PM, Ana Marija wrote: > > > > > Hi Jim, > > > > > > > > > > thank you so much for getting back to me. I tried your code and this > > > > > is > > > > > what I get: > > > > >> dim(neu2) > > > > > [1] 3740988 9 > > > > >> dim(nep2) > > > > > [1] 3740988 9 > > > > >> dim(ret2) > > > > > [1] 3740001 9 > > > > > > > > > > I think I would need to have the same number of lines in all 3 data > > > > > frames. > > > > > > > > > > Can you please advise. > > > > > > > > > > > > You should check for duplicated Marker values. > > > > > > > > > > > > -- > > > > > > > > David > > > > > > > > > > > > > > Cheers > > > > > Ana > > > > > > > > > > On Mon, Jun 1, 2020 at 7:31 PM Jim Lemon <[email protected]> wrote: > > > > > > > > > >> Hi Ana, > > > > >> Not too hard, but your example has all the "marker" fields in common. > > > > >> So using a sample that will show the expected result: > > > > >> > > > > >> neu1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N > > > > >> 1 100000012 1:100000012:G:T 0.229925 T G + 0.650403 1594 > > > > >> 1 100000827 1:100000827:C:T 0.287014 T C + 0.955449 1594 > > > > >> 1 100002713 1:100002713:C:T 0.097867 T C - 0.290455 1594 > > > > >> 1 100002882 1:100002882:T:G 0.287014 G T + 0.955449 1594 > > > > >> 1 100002991 1:100002991:G:A 0.097867 A G - 0.290455 1594 > > > > >> 1 100004726 1:100004726:G:A 0.132058 A G + 0.115005 1594", > > > > >> header=TRUE,stringsAsFactors=FALSE) > > > > >> > > > > >> nep1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N > > > > >> 1 100000012 1:100000012:G:T 0.2300430 T G - 0.1420030 1641 > > > > >> 1 100000827 1:100000827:C:T 0.2867150 T C - 0.2045580 1641 > > > > >> 1 100002713 1:100002713:C:T 0.0975015 T C - 0.0555507 1641 > > > > >> 1 100002882 1:100002882:T:G 0.2867150 G T - 0.2045580 1641 > > > > >> 1 100002991 1:100002991:G:A 0.0975015 A G - 0.0555507 1641 > > > > >> 1 100004726 1:100004727:G:A 0.1325410 A G - 0.8725660 1641", > > > > >> header=TRUE,stringsAsFactors=FALSE) > > > > >> > > > > >> ret1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N > > > > >> 1 100000012 1:100000012:G:T 0.2322760 T G - 0.230383 1608 > > > > >> 1 100000827 1:100000827:C:T 0.2882460 T C - 0.120356 1608 > > > > >> 1 100002713 1:100002713:C:T 0.0982587 T C - 0.272936 1608 > > > > >> 1 100002882 1:100002882:T:G 0.2882460 G T - 0.120356 1608 > > > > >> 1 100002991 1:100002992:G:A 0.0982587 A G - 0.272936 1608 > > > > >> 1 100004726 1:100004727:G:A 0.1340170 A G - 0.594538 1608", > > > > >> header=TRUE,stringsAsFactors=FALSE) > > > > >> > > > > >> # merge the three data frames on "Marker" > > > > >> nn1<-merge(neu1,nep1,by="Marker") > > > > >> nn2<-merge(nn1,ret1,by="Marker") > > > > >> # get the common "Marker" strings > > > > >> Marker3<-nn2$Marker > > > > >> # subset all three data frames on Marker3 > > > > >> neu2<-neu1[neu1$Marker %in% Marker3,] > > > > >> nep2<-nep1[nep1$Marker %in% Marker3,] > > > > >> ret2<-ret1[ret1$Marker %in% Marker3,] > > > > >> > > > > >> Jim > > > > >> > > > > >> On Tue, Jun 2, 2020 at 7:50 AM Ana Marija > > > > >> <[email protected]> > > > > >> wrote: > > > > >>> Hello, > > > > >>> > > > > >>> I have 3 data frames which have about 3.4 mill lines (but they > > > > >>> don't have > > > > >>> exactly the same number of lines)...they look like this: > > > > >>> ... > > > > >>> Is there is a way to create another 3 data frames, say neu2, nep2, > > > > >>> ret2 > > > > >>> which would only contain lines that have the same entries in Marker > > > > >> column > > > > >>> for all 3 data frames? > > > > >>> > > > > >>> Thanks > > > > >>> Ana > > > > >>> > > > > >>> [[alternative HTML version deleted]] > > > > >>> > > > > >>> ______________________________________________ > > > > >>> [email protected] 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]] > > > > > > > > > > ______________________________________________ > > > > > [email protected] 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. ______________________________________________ [email protected] 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.
