[R] opening files in directory
Hi there
I want to be able to take all the files in a given directory, read them in one
at a time, calculate a distance matrix for them (the files are data matrices)
and then print them out to separate files. This is the code I thought I would
be able to use
(all files are in directory data_files)
for(i in 1:length(files))
+ {
+ x-read.table(data_files/files[[i]])
+ dist-dist(x, method=euclidean, diag=TRUE)
+ mat-as.matrix(dist)
+ write.table(mat, file=files[[i]])
+ }
But I get this error when I try to open the first file using read.table
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'data_files/files[[i]]'
if I try the read.table command without the quotation marks like so
x-read.table(data_matrix_files/files[[i]])
I get the error
Error in read.table(data_matrix_files/files[[i]]) :
Object data_matrix_files not found
But if I go to the directory where the files are kept before starting up R, the
read.table command without the quotation marks works.
I don't want to start up R in the same directory as the where the files I will
be using reside though so how do I rectify this?
Any help much appreciated
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Re: [R] opening files in directory
FAQ ...
Uwe Ligges
Ffenics wrote:
Hi there
I want to be able to take all the files in a given directory, read them in
one at a time, calculate a distance matrix for them (the files are data
matrices) and then print them out to separate files. This is the code I
thought I would be able to use
(all files are in directory data_files)
for(i in 1:length(files))
+ {
+ x-read.table(data_files/files[[i]])
+ dist-dist(x, method=euclidean, diag=TRUE)
+ mat-as.matrix(dist)
+ write.table(mat, file=files[[i]])
+ }
But I get this error when I try to open the first file using read.table
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'data_files/files[[i]]'
if I try the read.table command without the quotation marks like so
x-read.table(data_matrix_files/files[[i]])
I get the error
Error in read.table(data_matrix_files/files[[i]]) :
Object data_matrix_files not found
But if I go to the directory where the files are kept before starting up R,
the read.table command without the quotation marks works.
I don't want to start up R in the same directory as the where the files I
will be using reside though so how do I rectify this?
Any help much appreciated
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
Re: [R] opening files in directory
Yes, already looked at the FAQ. Thats how I have got where I am.
I didnt see a solution to this particular problem on there though
Thanks anyway.
Uwe Ligges [EMAIL PROTECTED] wrote: FAQ ...
Uwe Ligges
Ffenics wrote:
Hi there
I want to be able to take all the files in a given directory, read them in
one at a time, calculate a distance matrix for them (the files are data
matrices) and then print them out to separate files. This is the code I
thought I would be able to use
(all files are in directory data_files)
for(i in 1:length(files))
+ {
+ x-read.table(data_files/files[[i]])
+ dist-dist(x, method=euclidean, diag=TRUE)
+ mat-as.matrix(dist)
+ write.table(mat, file=files[[i]])
+ }
But I get this error when I try to open the first file using read.table
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'data_files/files[[i]]'
if I try the read.table command without the quotation marks like so
x-read.table(data_matrix_files/files[[i]])
I get the error
Error in read.table(data_matrix_files/files[[i]]) :
Object data_matrix_files not found
But if I go to the directory where the files are kept before starting up R,
the read.table command without the quotation marks works.
I don't want to start up R in the same directory as the where the files I
will be using reside though so how do I rectify this?
Any help much appreciated
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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.
Re: [R] opening files in directory
R won't do variable interpolation inside quotation marks as perl does.
You could try amending your code with, for e.g.
file.name-paste(sep=/,data_files,files[[i]])
x-read.table(file.name)
Regards,
Mike
On 9/4/06, Ffenics [EMAIL PROTECTED] wrote:
Hi there
I want to be able to take all the files in a given directory, read them in
one at a time, calculate a distance matrix for them (the files are data
matrices) and then print them out to separate files. This is the code I
thought I would be able to use
(all files are in directory data_files)
for(i in 1:length(files))
+ {
+ x-read.table(data_files/files[[i]])
+ dist-dist(x, method=euclidean, diag=TRUE)
+ mat-as.matrix(dist)
+ write.table(mat, file=files[[i]])
+ }
But I get this error when I try to open the first file using read.table
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file 'data_files/files[[i]]'
if I try the read.table command without the quotation marks like so
x-read.table(data_matrix_files/files[[i]])
I get the error
Error in read.table(data_matrix_files/files[[i]]) :
Object data_matrix_files not found
But if I go to the directory where the files are kept before starting up R,
the read.table command without the quotation marks works.
I don't want to start up R in the same directory as the where the files I
will be using reside though so how do I rectify this?
Any help much appreciated
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
--
Regards,
Mike Nielsen
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] opening files in directory
On 9/4/06, Mike Nielsen [EMAIL PROTECTED] wrote: R won't do variable interpolation inside quotation marks as perl does. Just as an aside, gsubfn in package gsubfn will do perl-style (well, sort of) string interpolation: library(gsubfn) i - 1 gsubfn(x = data_files/file$i) [1] data_files/file1 cati and cati0 in the same package provide for such interpolation within cat. __ R-help@stat.math.ethz.ch 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.
