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 <[email protected]>
To: [email protected]
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: [email protected]
> Subject: Re: [R] extracting rows and columns from a big matrix
> To: [email protected]
>
> 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 <[email protected]>
> To: [email protected]
> Cc: [email protected]
> 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: [email protected]
> > Subject: Re: [R] extracting rows and columns from a big matrix
> > To: [email protected]
> > CC: [email protected]
> >
> > 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 <[email protected]>
> > To: [email protected]
> > Cc: [email protected]
> > 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: [email protected]
> > > Subject: Re: [R] extracting rows and columns from a big matrix
> > > To: [email protected]
> > > CC: [email protected]
> > >
> > > 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 <[email protected]>
> > > To: [email protected]
> > > Cc: [email protected]
> > > 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: [email protected]
> > > > To: [email protected]
> > > > CC: [email protected]
> > > >
> > > > 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 <[email protected]> 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]]
> > > > >
> > > > > ______________________________________________
> > > > > [email protected] 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.
> > >
> > > ______________________________________________
> > > [email protected] 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.
> > >
______________________________________________
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