R help - Jul 2008 - Read.table - Less rows than original data

Dear all,

I have problem when reading a table into R. The total row of read in table
has is much less than the original saved table.

I built a 1,273,230 by 6 data set named "mydata2", it was saved in the
following command,

write.table(mydata2, "mydata2.txt",
row.name=F,col.name=T,quote=F,sep="\t")

The next day I read in above saved text file into R,

temp<-read.table("mydata2.txt",header=T,sep="\t",na.strings="NA")

However, the dimension of "temp" is 636,615 X 6.

Do yo know why?

Thanks for your attention.

Sityee

	[[alternative HTML version deleted]]

phoebe kong <sityeekong <at> gmail.com> writes:
> I built a 1,273,230 by 6 data set named "mydata2", it was saved
in the
> following command,
> 
> write.table(mydata2, "mydata2.txt",
row.name=F,col.name=T,quote=F,sep="\t")
> 
> The next day I read in above saved text file into R,
> 
>
temp<-read.table("mydata2.txt",header=T,sep="\t",na.strings="NA")
> 
> However, the dimension of "temp" is 636,615 X 6.

  A long shot: do you by any chance have any "#" characters
in your data set?  If they all occurred for the first time
in column number 636,616 that would produce the observed
problem.  If so, set comment.char="".  

  Does this happen if you generate a random data set?

  Ben Bolker

> I built a 1,273,230 by 6 data set named "mydata2", it was saved
in the
> following command,
> 
> write.table(mydata2, "mydata2.txt",
row.name=F,col.name=T,quote=F,sep="\t")
> 
> The next day I read in above saved text file into R,
> 
>
temp<-read.table("mydata2.txt",header=T,sep="\t",na.strings="NA")
> 
> However, the dimension of "temp" is 636,615 X 6.

A wild guess: does your table contain strings which include single or
double ticks? As you are not disabling quoting in read.table this can
cause problems:
> foo = data.frame(a=c("abc","5'foo","xxx",
"3'bar"), b=1:4)
> foo
      a b
1   abc 1
2 5'foo 2
3   xxx 3
4 3'bar 4
> write.table(foo, "mydata2.txt",
row.name=F,col.name=T,quote=F,sep="\t")
> foo <-
read.table("mydata2.txt",header=T,sep="\t",na.strings="NA")
> foo
                      a b
1                   abc 1
2 5foo\t2\nxxx\t3\n3bar 4
> foo <-
read.table("mydata2.txt",header=T,sep="\t",na.strings="NA",
quote='')
> foo
      a b
1   abc 1
2 5'foo 2
3   xxx 3
4 3'bar 4


The same aplies to comment characters embedded in strings.

If this is not your problem, I'd first check if the file has the
expected number of lines.

cu
	Philipp

-- 
Dr. Philipp Pagel
Lehrstuhl f?r Genomorientierte Bioinformatik
Technische Universit?t M?nchen
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://mips.gsf.de/staff/pagel