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-boun...@r-project.org per conto di Daniel Nordlund
Inviato: lun 06/07/2009 20.45
A: r-h...@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-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of mau...@alice.it
> Sent: Sunday, July 05, 2009 11:28 PM
> To: Martin Morgan
> Cc: r-h...@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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