R help - Feb 2012 - Problems reading tab-delim files using read.table and read.delim

Hello,

I used read.xlsx to read in Excel files but for large files it turned out to
be not very efficient.
For that reason I use a programme which writes each sheet in an Excel file
into tab-delim txt files.
After that I tried using read.table and read.delim to read in those txt
files. Unfortunately, the results
are not as expected. To show you what I mean I created a tiny Excel sheet
with some rows and columns and
read it in using read.xlsx. I also used my script to write that sheet to a
tab-delim txt file and read that one it with
read.table and read.delim. Here is the R output:


> (test <- read.table(Sheet1.txt, header=TRUE, sep="\t"))
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, 
: 
  line 1 did not have 5 elements
> (test <- read.delim(Sheet1.txt, header=TRUE, sep="\t"))
     c1 c2 c3  X
123 213 NA NA NA
234 asd NA NA NA
> (test <- read.xlsx(file.path(data), "Sheet1"))
   c1   c2  c3       NA.     NA..1     NA..2
1 123 <NA> 213                <NA>      <NA>
2 234  asd  NA      <NA>                    


The last output is what I would expect the file to be read in. Columns 4 to
6 do not have any header rows. in R1C4 I added some white spaces as well as
into R2C5 and R2C6 which a read in correctly by the read.xlsx function.

read.table and read.delim seem not to be able to handle such files. Is there
any workaround for that?


Cheers

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I don't know if this completely solves your problem, but here are some  
arguments to read.table/read.delim you might try:
row.names=FALSE
fill=TRUE
The details section also suggests using the colClasses argument as the  
number of columns is determined from the first 5 rows which may not be  
correct.

HTH

Jan



mails <mails00000 at gmail.com> schreef:
> Hello,
>
> I used read.xlsx to read in Excel files but for large files it turned out
to
> be not very efficient.
> For that reason I use a programme which writes each sheet in an Excel file
> into tab-delim txt files.
> After that I tried using read.table and read.delim to read in those txt
> files. Unfortunately, the results
> are not as expected. To show you what I mean I created a tiny Excel sheet
> with some rows and columns and
> read it in using read.xlsx. I also used my script to write that sheet to a
> tab-delim txt file and read that one it with
> read.table and read.delim. Here is the R output:
>
>
>
>> (test <- read.table(Sheet1.txt, header=TRUE, sep="\t"))
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>   line 1 did not have 5 elements
>
>> (test <- read.delim(Sheet1.txt, header=TRUE, sep="\t"))
>      c1 c2 c3  X
> 123 213 NA NA NA
> 234 asd NA NA NA
>
>> (test <- read.xlsx(file.path(data), "Sheet1"))
>    c1   c2  c3       NA.     NA..1     NA..2
> 1 123 <NA> 213                <NA>      <NA>
> 2 234  asd  NA      <NA>
>
>
> The last output is what I would expect the file to be read in. Columns 4 to
> 6 do not have any header rows. in R1C4 I added some white spaces as well as
> into R2C5 and R2C6 which a read in correctly by the read.xlsx function.
>
> read.table and read.delim seem not to be able to handle such files. Is
there
> any workaround for that?
>
>
> Cheers
>
> --
> View this message in context:  
>
http://r.789695.n4.nabble.com/Problems-reading-tab-delim-files-using-read-table-and-read-delim-tp4369195p4369195.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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.

On Wed, Feb 8, 2012 at 7:09 AM, mails <mails00000 at gmail.com>
wrote:
> Hello,
>
> I used read.xlsx to read in Excel files but for large files it turned out
to
> be not very efficient.
> For that reason I use a programme which writes each sheet in an Excel file
> into tab-delim txt files.
Note that that is how read.xls in the gdata package works - it uses a
perl program to convert the spreadsheet to a text file and then reads
in the text file.

-- 
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