[R] Not all rows are being read-in

[Dimitri Liakhovitski]

Philipp, you are a savior!
That's exactly what has been happening - and it was driving me crazy.
quote="" fixed things.
Thank you very much!
Dimitri

On Wed, Mar 30, 2011 at 5:01 AM, Philipp Pagel <p.pagel at wzw.tum.de> wrote:
> 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/
>
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>



-- 
Dimitri Liakhovitski
Ninah Consulting
www.ninah.com