Hi Bogdan, Kinda messy, but: N <- data.frame(N=c("n1","n2","n3","n4")) M <- data.frame(M=c("m1","m2","m3","m4","m5")) C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) names(MN)<-M[,1] rownames(MN)<-N[,1] C[,1]<-as.character(C[,1]) C[,2]<-as.character(C[,2]) for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3] Jim On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote:> Dear Bert, > > thank you for your response. here it is the piece of R code : given 3 data > frames below --- > > N <- data.frame(N=c("n1","n2","n3","n4")) > > M <- data.frame(M=c("m1","m2","m3","m4","m5")) > > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) > > how shall I integrate N, and M, and C in such a way that at the end we have > a data frame with : > > > - list N as the columns names > - list M as the rows names > - the values in the cells of N * M, corresponding to the numerical > values in the data frame C. > > more precisely, the result shall be : > > n1 n2 n3 n4 > m1 100 200 - - > m2 - - - - > m3 - - 300 - > m4 - - - - > m5 - - - - > > thank you ! > > > On Mon, Jun 5, 2017 at 6:57 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > >> Reproducible example, please. -- In particular, what exactly does C look >> ilike? >> >> (You should know this by now). >> >> -- Bert >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along >> and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: >> > Dear all, >> > >> > please could you advise on the R code I could use in order to do the >> > following operation : >> > >> > a. -- I have 2 lists of "genome coordinates" : a list is composed by >> > numbers that represent genome coordinates; >> > >> > let's say list N : >> > >> > n1 >> > >> > n2 >> > >> > n3 >> > >> > n4 >> > >> > and a list M: >> > >> > m1 >> > >> > m2 >> > >> > m3 >> > >> > m4 >> > >> > m5 >> > >> > 2 -- and a data frame C, where for some pairs of coordinates (n,m) from >> the >> > lists above, we have a numerical intensity; >> > >> > for example : >> > >> > n1; m1; 100 >> > >> > n1; m2; 300 >> > >> > The question would be : what is the most efficient R code I could use in >> > order to integrate the list N, the list M, and the data frame C, in order >> > to obtain a DATA FRAME, >> > >> > -- list N as the columns names >> > -- list M as the rows names >> > -- the values in the cells of N * M, corresponding to the numerical >> values >> > in the data frame C. >> > >> > A little example would be : >> > >> > n1 n2 n3 n4 >> > >> > m1 100 - - - >> > >> > m2 300 - - - >> > >> > m3 - - - - >> > >> > m4 - - - - >> > >> > m5 - - - - >> > I wrote a script in perl, although i would like to do this in R >> > Many thanks ;) >> > -- bogdan >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-help at 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 at 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.

Thank you Jim ! On Tue, Jun 6, 2017 at 4:01 AM, Jim Lemon <drjimlemon at gmail.com> wrote:> Hi Bogdan, > Kinda messy, but: > > N <- data.frame(N=c("n1","n2","n3","n4")) > M <- data.frame(M=c("m1","m2","m3","m4","m5")) > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), > I=c(100,300,400)) > MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) > names(MN)<-M[,1] > rownames(MN)<-N[,1] > C[,1]<-as.character(C[,1]) > C[,2]<-as.character(C[,2]) > for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3] > > Jim > > On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > > Dear Bert, > > > > thank you for your response. here it is the piece of R code : given 3 > data > > frames below --- > > > > N <- data.frame(N=c("n1","n2","n3","n4")) > > > > M <- data.frame(M=c("m1","m2","m3","m4","m5")) > > > > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), > I=c(100,300,400)) > > > > how shall I integrate N, and M, and C in such a way that at the end we > have > > a data frame with : > > > > > > - list N as the columns names > > - list M as the rows names > > - the values in the cells of N * M, corresponding to the numerical > > values in the data frame C. > > > > more precisely, the result shall be : > > > > n1 n2 n3 n4 > > m1 100 200 - - > > m2 - - - - > > m3 - - 300 - > > m4 - - - - > > m5 - - - - > > > > thank you ! > > > > > > On Mon, Jun 5, 2017 at 6:57 PM, Bert Gunter <bgunter.4567 at gmail.com> > wrote: > > > >> Reproducible example, please. -- In particular, what exactly does C look > >> ilike? > >> > >> (You should know this by now). > >> > >> -- Bert > >> Bert Gunter > >> > >> "The trouble with having an open mind is that people keep coming along > >> and sticking things into it." > >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > >> > >> > >> On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > >> > Dear all, > >> > > >> > please could you advise on the R code I could use in order to do the > >> > following operation : > >> > > >> > a. -- I have 2 lists of "genome coordinates" : a list is composed by > >> > numbers that represent genome coordinates; > >> > > >> > let's say list N : > >> > > >> > n1 > >> > > >> > n2 > >> > > >> > n3 > >> > > >> > n4 > >> > > >> > and a list M: > >> > > >> > m1 > >> > > >> > m2 > >> > > >> > m3 > >> > > >> > m4 > >> > > >> > m5 > >> > > >> > 2 -- and a data frame C, where for some pairs of coordinates (n,m) > from > >> the > >> > lists above, we have a numerical intensity; > >> > > >> > for example : > >> > > >> > n1; m1; 100 > >> > > >> > n1; m2; 300 > >> > > >> > The question would be : what is the most efficient R code I could use > in > >> > order to integrate the list N, the list M, and the data frame C, in > order > >> > to obtain a DATA FRAME, > >> > > >> > -- list N as the columns names > >> > -- list M as the rows names > >> > -- the values in the cells of N * M, corresponding to the numerical > >> values > >> > in the data frame C. > >> > > >> > A little example would be : > >> > > >> > n1 n2 n3 n4 > >> > > >> > m1 100 - - - > >> > > >> > m2 300 - - - > >> > > >> > m3 - - - - > >> > > >> > m4 - - - - > >> > > >> > m5 - - - - > >> > I wrote a script in perl, although i would like to do this in R > >> > Many thanks ;) > >> > -- bogdan > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > ______________________________________________ > >> > R-help at 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 at 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]]

Here's another approach: N <- data.frame(N=c("n1","n2","n3","n4")) M <- data.frame(M=c("m1","m2","m3","m4","m5")) C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) # Rebuild the factors using M and N C$m <- factor(as.character(C$m), levels=levels(M$M)) C$n <- factor(as.character(C$n), levels=levels(N$N)) MN <- xtabs(I~m+n, C) print(MN, zero.print="-") # n # m n1 n2 n3 n4 # m1 100 300 - - # m2 - - - - # m3 - - 400 - # m4 - - - - # m5 - - - - class(MN) # [1] "xtabs" "table" # MN is a table. If you want a data.frame MN <- as.data.frame.matrix(MN) class(MN) # [1] "data.frame" ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Jim Lemon Sent: Tuesday, June 6, 2017 6:02 AM To: Bogdan Tanasa <tanasa at gmail.com>; r-help mailing list <r-help at r-project.org> Subject: Re: [R] integrating 2 lists and a data frame in R Hi Bogdan, Kinda messy, but: N <- data.frame(N=c("n1","n2","n3","n4")) M <- data.frame(M=c("m1","m2","m3","m4","m5")) C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) names(MN)<-M[,1] rownames(MN)<-N[,1] C[,1]<-as.character(C[,1]) C[,2]<-as.character(C[,2]) for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3] Jim On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote:> Dear Bert, > > thank you for your response. here it is the piece of R code : given 3 data > frames below --- > > N <- data.frame(N=c("n1","n2","n3","n4")) > > M <- data.frame(M=c("m1","m2","m3","m4","m5")) > > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) > > how shall I integrate N, and M, and C in such a way that at the end we have > a data frame with : > > > - list N as the columns names > - list M as the rows names > - the values in the cells of N * M, corresponding to the numerical > values in the data frame C. > > more precisely, the result shall be : > > n1 n2 n3 n4 > m1 100 200 - - > m2 - - - - > m3 - - 300 - > m4 - - - - > m5 - - - - > > thank you ! > > > On Mon, Jun 5, 2017 at 6:57 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > >> Reproducible example, please. -- In particular, what exactly does C look >> ilike? >> >> (You should know this by now). >> >> -- Bert >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along >> and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: >> > Dear all, >> > >> > please could you advise on the R code I could use in order to do the >> > following operation : >> > >> > a. -- I have 2 lists of "genome coordinates" : a list is composed by >> > numbers that represent genome coordinates; >> > >> > let's say list N : >> > >> > n1 >> > >> > n2 >> > >> > n3 >> > >> > n4 >> > >> > and a list M: >> > >> > m1 >> > >> > m2 >> > >> > m3 >> > >> > m4 >> > >> > m5 >> > >> > 2 -- and a data frame C, where for some pairs of coordinates (n,m) from >> the >> > lists above, we have a numerical intensity; >> > >> > for example : >> > >> > n1; m1; 100 >> > >> > n1; m2; 300 >> > >> > The question would be : what is the most efficient R code I could use in >> > order to integrate the list N, the list M, and the data frame C, in order >> > to obtain a DATA FRAME, >> > >> > -- list N as the columns names >> > -- list M as the rows names >> > -- the values in the cells of N * M, corresponding to the numerical >> values >> > in the data frame C. >> > >> > A little example would be : >> > >> > n1 n2 n3 n4 >> > >> > m1 100 - - - >> > >> > m2 300 - - - >> > >> > m3 - - - - >> > >> > m4 - - - - >> > >> > m5 - - - - >> > I wrote a script in perl, although i would like to do this in R >> > Many thanks ;) >> > -- bogdan >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-help at 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 at 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 at 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.

> On Jun 6, 2017, at 4:01 AM, Jim Lemon <drjimlemon at gmail.com> wrote: > > Hi Bogdan, > Kinda messy, but: > > N <- data.frame(N=c("n1","n2","n3","n4")) > M <- data.frame(M=c("m1","m2","m3","m4","m5")) > C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) > MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) > names(MN)<-M[,1] > rownames(MN)<-N[,1] > C[,1]<-as.character(C[,1]) > C[,2]<-as.character(C[,2]) > for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3]`xtabs` offers another route: C$m <- factor(C$m, levels=M$M) C$n <- factor(C$n, levels=N$N) Option 1: Zeroes in the empty positions:> (X <- xtabs(I ~ m+n , C, addNA=TRUE))n m n1 n2 n3 n4 m1 100 300 0 0 m2 0 0 0 0 m3 0 0 400 0 m4 0 0 0 0 m5 0 0 0 0 Option 2: Sparase matrix> (X <- xtabs(I ~ m+n , C, sparse=TRUE))5 x 4 sparse Matrix of class "dgCMatrix" n m n1 n2 n3 n4 m1 100 300 . . m2 . . . . m3 . . 400 . m4 . . . . m5 . . . . I wasn't sure if the sparse reuslts of xtabs would make a distinction between 0 and NA, but happily it does:> C <- data.frame(n=c("n1","n2","n3", "n3", "n4"), m=c("m1","m1","m3", "m4", "m5"), I=c(100,300,400, NA, 0)) > Cn m I 1 n1 m1 100 2 n2 m1 300 3 n3 m3 400 4 n3 m4 NA 5 n4 m5 0> (X <- xtabs(I ~ m+n , C, sparse=TRUE))4 x 4 sparse Matrix of class "dgCMatrix" n m n1 n2 n3 n4 m1 100 300 . . m3 . . 400 . m4 . . . . m5 . . . 0 (In the example I forgot to repeat the lines that augmented the factor levels so m2 is not seen. -- Davod> > > Jim > > On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: >> Dear Bert, >> >> thank you for your response. here it is the piece of R code : given 3 data >> frames below --- >> >> N <- data.frame(N=c("n1","n2","n3","n4")) >> >> M <- data.frame(M=c("m1","m2","m3","m4","m5")) >> >> C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"), I=c(100,300,400)) >> >> how shall I integrate N, and M, and C in such a way that at the end we have >> a data frame with : >> >> >> - list N as the columns names >> - list M as the rows names >> - the values in the cells of N * M, corresponding to the numerical >> values in the data frame C. >> >> more precisely, the result shall be : >> >> n1 n2 n3 n4 >> m1 100 200 - - >> m2 - - - - >> m3 - - 300 - >> m4 - - - - >> m5 - - - - >> >> thank you ! >> >> >> On Mon, Jun 5, 2017 at 6:57 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote: >> >>> Reproducible example, please. -- In particular, what exactly does C look >>> ilike? >>> >>> (You should know this by now). >>> >>> -- Bert >>> Bert Gunter >>> >>> "The trouble with having an open mind is that people keep coming along >>> and sticking things into it." >>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >>> >>> >>> On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: >>>> Dear all, >>>> >>>> please could you advise on the R code I could use in order to do the >>>> following operation : >>>> >>>> a. -- I have 2 lists of "genome coordinates" : a list is composed by >>>> numbers that represent genome coordinates; >>>> >>>> let's say list N : >>>> >>>> n1 >>>> >>>> n2 >>>> >>>> n3 >>>> >>>> n4 >>>> >>>> and a list M: >>>> >>>> m1 >>>> >>>> m2 >>>> >>>> m3 >>>> >>>> m4 >>>> >>>> m5 >>>> >>>> 2 -- and a data frame C, where for some pairs of coordinates (n,m) from >>> the >>>> lists above, we have a numerical intensity; >>>> >>>> for example : >>>> >>>> n1; m1; 100 >>>> >>>> n1; m2; 300 >>>> >>>> The question would be : what is the most efficient R code I could use in >>>> order to integrate the list N, the list M, and the data frame C, in order >>>> to obtain a DATA FRAME, >>>> >>>> -- list N as the columns names >>>> -- list M as the rows names >>>> -- the values in the cells of N * M, corresponding to the numerical >>> values >>>> in the data frame C. >>>> >>>> A little example would be : >>>> >>>> n1 n2 n3 n4 >>>> >>>> m1 100 - - - >>>> >>>> m2 300 - - - >>>> >>>> m3 - - - - >>>> >>>> m4 - - - - >>>> >>>> m5 - - - - >>>> I wrote a script in perl, although i would like to do this in R >>>> Many thanks ;) >>>> -- bogdan >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> R-help at 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 at 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 at 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.David Winsemius Alameda, CA, USA