It works if the web file adress is of the type:  "http://".
It does not work if the web file adress is of the type:  "'ftp://".
> outFile <- read.xls("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls")
Error in xls2csv(xls, sheet, verbose = verbose, ..., perl = perl) : 
  Unable to read xls file 'ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls'.
Error in file.exists(tfn) : invalid 'file' argument

But the file does exists as shown in the following:
> download.file("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls","outFile")
trying URL 'ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls'
ftp data connection made, file length 2563072 bytes
opened URL
downloaded 2.4 Mb

Can the two steps (download + read.xls) be performed with one command line  only ?

Thank you,
Maura



-----Messaggio originale-----
Da: r-help-bounces@r-project.org per conto di Daniel Nordlund
Inviato: lun 06/07/2009 20.45
A: r-help@stat.math.ethz.ch
Oggetto: Re: [R] R: R: Is there a way to extract some fields data fromHTML	pages through any R function ?
 
> -----Original Message-----
> From: r-help-bounces@r-project.org 
> [mailto:r-help-bounces@r-project.org] On Behalf Of mauede@alice.it
> Sent: Sunday, July 05, 2009 11:28 PM
> To: Martin Morgan
> Cc: r-help@stat.math.ethz.ch
> Subject: [R] R: R: Is there a way to extract some fields data 
> from HTML pages through any R function ?
> 
> It helps. But it is overly sophisticated.
> I have already downloaded and used the Excel file containing 
> the validated stuff.
> 
> Since there are R commands to download gzip as well as FASTA 
> files, I wonder whether it is possible to 
> automatically download the Excel file from 
> http://mirecords.umn.edu/miRecords/download.php
> Actually the latter may not be the actual file URL because it 
> is necessary to click on the word "here" to download the file.
> 
> Thank you,
> Maura
> 
Maura,

I haven't seen a response to your question (however, I just may have missed
it, or you mave have received an off-line response).  I went to the URL
above and found that the Excel file is at

http://mirecords.umn.edu/miRecords/download_data.php?v=1

I think you could use the read.xls() function from the gdata package to get
the file, something like this

library(gdata)
df <- read.xls("http://mirecords.umn.edu/miRecords/download_data.php?v=1")

Hope this is helpful,

Dan

Daniel Nordlund
Bothell, WA USA

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