I guess R is enough poweful to subset greater than 300x300. But if it is a problem regarding dataset I am wondering why codes are working splitting the 1788 journal label set into 6 groups of around 300 labels... Summarizing: if you put the whole set it doesn't work. If you divide into groups of around 300 labels, it does.
I keep thinking it's a liitle bit strange. I have checked labels from matrix and there is not any inconsistency I will try to get different groups and then I will join them with "merge" function. I think maybe not the best solution, but at least, I hope it works. Thanks everybody! AJ > Date: Mon, 16 Jul 2012 09:08:15 -0700 > From: smartpink...@yahoo.com > Subject: Re: [R] extracting rows and columns from a big matrix > To: anxu...@hotmail.com > CC: r-help@r-project.org > > Hi, > > If you think that R may not be able to subset greater than 300X300, > > Try this: > m<-matrix(numeric(350*2000),ncol=2000) > colnames(m)<-paste("X",1:2000,sep="") > rownames(m)<-paste("X",1:350,sep="") > m[c("X6","X20","X151","X180"),c("X25","X150","X1500","X1750")] > X25 X150 X1500 X1750 > X6 0 0 0 0 > X20 0 0 0 0 > X151 0 0 0 0 > X180 0 0 0 0 > > > > #So, I guess there might be some problems in your dataset. > > A.K. > > > > > > ________________________________ > From: A J <anxu...@hotmail.com> > To: smartpink...@yahoo.com > Sent: Monday, July 16, 2012 10:37 AM > Subject: RE: [R] extracting rows and columns from a big matrix > > > > Hello again! > > > Sorry for the inconvenience and thanks to everybody trying to help me. The > steps I followed in the proccess are thoses: > > > 1) Open the .csv file containing the large matrix (15000 rows x 15000 > columns) using write.table > 2) If I try to subset the total number of columns and/or rows that I need, > just 1788 ones (resulting a new square submatrix), R don't permit to do it > and at the end of the console return the "+" sign > 3) In order to check there is no mistakes I have copied labels from the .csv > file and I have compared with the original database comprising all the data. > There is no mistakes. > 4) After seeing all data in Excel I decided to split the number of columns > that I need to subset it in different parts. Developing several tests, I have > checked that R works if the number of columns that I require is not higher > than 300 (maybe a little bit higher, but I don't want to waste time executing > so many tests). > 5) I have thought the best solution maybe to divide data in different groups > of around 300 rows x 300 colums submatrices and then, join them using, for > instance, "merge" function to get the final square submatrix of 1788 x 1788. > > > I think all is really strange, but I have developed several tests and > different methods and I can't find a good and consistent argument. Perhaps > label length have some connection, but I am not sure. I will inform about the > results. > > > Greetings and thanks again > > > AJ > > > > Date: Mon, 16 Jul 2012 07:05:44 -0700 > > From: smartpink...@yahoo.com > > Subject: Re: [R] extracting rows and columns from a big matrix > > To: anxu...@hotmail.com > > > > Hello AJ, > > > > If I understand your email, there is no problem in subsetting n (say 300 or > > 400) number of columns from the 1st and 2nd splitted ones (447 columns). > > Try saving the third and fourth set using write.csv and open it in excel to > > see for any anomalies. How did you split the files? Is it after reading > > it in R? > > > > > > A.K. > > > > > > > > > > ________________________________ > > From: A J <anxu...@hotmail.com> > > To: smartpink...@yahoo.com > > Cc: r-help@r-project.org > > Sent: Monday, July 16, 2012 9:10 AM > > Subject: RE: [R] extracting rows and columns from a big matrix > > > > > > > > Yes, I have tried it and this works. > > > > > > Indeed, if I use a small number of colums, all the methods proposed here > > are working. Following the previous mail I have splited the number of > > colums in 4 parts of 447 colums each one. The first and the second ones > > work weel, but this doesn't occur with third and fourth parts. I am > > convinced it's not a problem with quotes, because I tried to remove them, > > and again the code in first and second part worked well. Now I have copied > > all labels directly from original matrix in txt file not to have any other > > mistakes. I will inform you about the enigmatic problem when I find it (I > > hope so...). > > > > > > Thanks for your comments and help. > > > > > > AJ > > > > > > > > > > > Date: Mon, 16 Jul 2012 05:46:46 -0700 > > > From: smartpink...@yahoo.com > > > Subject: Re: [R] extracting rows and columns from a big matrix > > > To: anxu...@hotmail.com > > > CC: r-help@r-project.org > > > > > > Hello, > > > > > > Have you tried subsetting smaller number of columns (say 5 or 6) from the > > > 2000 column dataset? If it is not working, then there might be problems > > > in reading the dataset. > > > > > > A.K. > > > > > > > > > > > > > > > ________________________________ > > > From: A J <anxu...@hotmail.com> > > > To: smartpink...@yahoo.com > > > Cc: r-help@r-project.org > > > Sent: Monday, July 16, 2012 6:49 AM > > > Subject: RE: [R] extracting rows and columns from a big matrix > > > > > > > > > > > > Thank you very much to everybody for your fast respones. > > > > > > > > > All your solutions are working well, but I keep with the same problem. > > > When I use whatever of your proposals with a small set of colums (and/or > > > rows), this work, but when I use the whole set of columns (and/or rows) > > > comprising around 2000 columns, the system don't return me the submatrix > > > specified and prompt sign ">" is replaced by "+" one at the end of the > > > console. May this be due to a limitation in subsetting matrices? > > > > > > > > > This is an example code working and using only columns: > > > > > > > > > m<-read.table("C:/backup/Rfiles/sym_matrix_cos.csv", header=T) > > > > > > > > > o<-as.matrix(m[(select=c("X12002", "X12027", "X12054", "X12084", > > > "X12085", "X12115", "X12129", "X12139", "X12195", "X12223", "X12295", > > > "X12327", "X12356", "X12474", "X12487", "X12491", "X12520", "X12570", > > > "X12600", "X12616", "X12626", "X12629", "X12634", "X12669", "X12685", > > > "X12748", "X12759", "X12766", "X12789", "X12793", "X12814", "X12824", > > > "X12892", "X12897", "X12909", "X12932", "X12959", "X12995", "X13018", > > > "X13039", "X13134", "X13138", "X13162", "X13173", "X13236", "X13243", > > > "X13351", "X13410", "X13452", "X13474", "X13475", "X13486", "X13518", > > > "X13574", "X13586", "X13588"))]) > > > > > > > > > > > > > > > > However, when I use the same code introducing the total number of columns > > > (around 2000) it's not working. > > > > > > > > > I have checked all labels several times in order not to commit mistakes. > > > For this reason I have copied and pasted all labels from a database to a > > > spreadsheet where I have added all quotes dragging them from the first > > > cell to last one (not to miss quotes). Really I don't have any idea about > > > the reason which R permits to apply this code taking 56 columns (as in > > > example above) and doesn't permit to do it taking around 2000 columns. If > > > you have any suggestions, please, let me know. > > > > > > > > > Thanks to everybody again. > > > > > > > > > Best, > > > > > > > > > AJ > > > > > > > > > > > > > Date: Sun, 15 Jul 2012 19:09:05 -0700 > > > > From: smartpink...@yahoo.com > > > > Subject: Re: [R] extracting rows and columns from a big matrix > > > > To: anxu...@hotmail.com > > > > CC: r-help@r-project.org > > > > > > > > Hello, > > > > > > > > In my previous email, I used index to subset the data. Then, I looked > > > > at your code. I guess you wanted to try the "subset" function to get > > > > the same output. > > > > > > > > Try this: > > > > dat1<-read.table(text=" > > > > X1 X7 X12 X15 X22 X26 X31 X34 X39 X44 X51 > > > > X1 1 2 3 4 5 6 7 8 9 10 11 > > > > X7 11 9 7 5 3 1 10 8 6 4 2 > > > > X12 3 4 7 8 5 7 2 9 1 3 2 > > > > X15 9 9 8 4 7 1 1 3 2 5 3 > > > > X22 6 7 7 4 4 2 9 8 8 1 1 > > > > X26 3 9 4 8 5 7 6 1 2 3 8 > > > > X31 1 2 1 3 1 4 1 5 1 6 1 > > > > X34 6 7 8 5 2 9 5 1 6 8 9 > > > > X39 4 8 7 4 6 5 1 9 2 7 5 > > > > X44 2 2 2 8 6 7 9 5 3 7 7 > > > > X51 9 9 9 6 6 4 8 7 2 1 3 > > > > ",sep="", header=TRUE) > > > > > > > > subset(dat1,subset=row.names(dat1)%in% > > > > c("X1","X12","X22","X31"),select=c("X1","X12","X22","X31")) > > > > X1 X12 X22 X31 > > > > X1 1 3 5 7 > > > > X12 3 7 5 2 > > > > X22 6 7 4 9 > > > > X31 1 1 1 1 > > > > > > > > A.K. > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: A J <anxu...@hotmail.com> > > > > To: jholt...@gmail.com > > > > Cc: r-help@r-project.org > > > > Sent: Sunday, July 15, 2012 3:43 PM > > > > Subject: Re: [R] extracting rows and columns from a big matrix > > > > > > > > > > > > Sorry so much for mistakes. > > > > > > > > It was an example code and I commited some mistakes typing it. But > > > > meaning the original code is right (I have checked several times) I am > > > > not sure about how to solve the problem of extracting columns and rows > > > > using labels from a squared matrix. I have enclosed a text file with > > > > the idea in order to understand it better. > > > > > > > > Thanks again, and sorry for the inconvenience. > > > > > > > > Best, > > > > > > > > AJ > > > > > > > > > > > > > > > > > Date: Sun, 15 Jul 2012 14:53:47 -0400 > > > > > Subject: Re: [R] extracting rows and columns from a big matrix > > > > > From: jholt...@gmail.com > > > > > To: anxu...@hotmail.com > > > > > CC: r-help@r-project.org > > > > > > > > > > For a start, you are missing a quote and a parenthese on the > > > > > statement; probably should be: (another quote was also missing) > > > > > > > > > > n<-subset(m, select=c("X1", "X7", "X12","X15", "X22", "X26", "X31", > > > > > "X34", "X39", "X44", "X51", "X58")) > > > > > > > > > > Not sure what you want with the rownames; an example would help and > > > > > post with 'dput'. > > > > > > > > > > On Sun, Jul 15, 2012 at 2:47 PM, A J <anxu...@hotmail.com> wrote: > > > > > > > > > > > > Hi there and thanks in advance. > > > > > > > > > > > > I have a large symmetrical matrix stored in a text file. After load > > > > > > in R I would like to extract the same number of columns and rows > > > > > > (symmetrical submatrix) using their labels. > > > > > > > > > > > > I have tried this code in order to extract columns, but R console > > > > > > gives me the "+" sign at the end of the code, pointing out > > > > > > incomplete command, so it is not working: > > > > > > > > > > > > m<-read.table("C:/backup/symmetrical.csv") > > > > > > > > > > > > n<-subset(m, select=c("X1", "X7", "X12", X15", "X22", "X26", "X31", > > > > > > "X34", "X39", "X44", "x51", "X58) > > > > > > > > > > > > Therefore, I have no tried with row names yet. > > > > > > > > > > > > Any suggestions? Sorry for the inconvenience. I have read some > > > > > > information about this but always have the same problem with "+" > > > > > > and I do not have any idea to follow. > > > > > > > > > > > > Best, > > > > > > > > > > > > AJ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > > > ______________________________________________ > > > > > > R-help@r-project.org mailing list > > > > > > 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. > > > > > > > > > > > > > > > > > > > > -- > > > > > Jim Holtman > > > > > Data Munger Guru > > > > > > > > > > What is the problem that you are trying to solve? > > > > > Tell me what you want to do, not how you want to do it. > > > > > > > > ______________________________________________ > > > > R-help@r-project.org mailing list > > > > 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 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.