[R] Not all rows are being read-in

[Philipp Pagel]

On Tue, Mar 29, 2011 at 06:58:59PM -0400, Dimitri Liakhovitski wrote:
> I have a tab-delimited .txt file (size 800MB) with about 3.4 million
> rows and 41 columns. About 15 columns contain strings.
> Tried to read it in in R 2.12.2 on a laptop that has Windows XP:
> mydata<-read.delim(file="FileName.TXT",sep="\t")
> R did not complain (!) and I got: dim(mydata) 1692063 41.

My guess would be that there are (unexpected) quotes and/or double quotes in your
file and so R thinks that rather large blocks of your file are
actually very long strings. This routinely happens in situations like
this:

ID      x   description
1     0.4   my first measurement  
2     1.6   Normal 5" object
3     0.4   Some measuremetn
4     0.7   A 4" long sample

R thinks that the description in row 2 ends in row 4 and you loose
data.

Try read.delim(..., quote="").

cu
	Philipp

-- 
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
Maximus-von-Imhof-Forum 3
85354 Freising, Germany
http://webclu.bio.wzw.tum.de/~pagel/