R help - Aug 2011 - Pb with \t interpretation in R

Hi,

I have to deal with a huge .txt table (~485.577 rows and 469 columns, > 1.5
Go file)
I used the read.table function
> tmp=read.table("data.txt", header=TRUE, sep="\t",
fill=TRUE,
na.strings="NA", comment.char="", stringsAsFactors = FALSE)
However, I encounter troubles in interpreting some "\t" separator.. A
column
displays \t\t\t\t characters fusioning consecutive columns and rows?
see:
"Body;3UTR\t\t\t\t\t\t\t\t\t\n3\tcg00000109\t59755374\t59755374\t0.8353283\t2657\t7\t7\t122.8385\t241.5193\t354\t2303\t0.00\t0.005"

Is there any way to deal with such problem?

Kind Regards
Sandrine
-- 

Sandrine Imbeaud
INSERM, UMR U-674, IUH
Université Paris Descartes
	
Génomique Fonctionnelle des tumeurs solides
27 rue Juliette Dodu
F75010 Paris, France
TEL: +33 (0)1 53 72 51 98
FAX: +33 (0)1 53 72 51 92
http://www.inserm-u674.net/

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On 29/08/2011 3:29 PM, Imbeaud (Inserm U674) wrote:
> Hi,
>
> I have to deal with a huge .txt table (~485.577 rows and 469 columns,> 
1.5
> Go file)
> I used the read.table function
> >  tmp=read.table("data.txt", header=TRUE, sep="\t",
fill=TRUE,
> na.strings="NA", comment.char="", stringsAsFactors =
FALSE)
> However, I encounter troubles in interpreting some "\t"
separator.. A column
> displays \t\t\t\t characters fusioning consecutive columns and rows?
> see:
>
"Body;3UTR\t\t\t\t\t\t\t\t\t\n3\tcg00000109\t59755374\t59755374\t0.8353283\t2657\t7\t7\t122.8385\t241.5193\t354\t2303\t0.00\t0.005"
>
> Is there any way to deal with such problem?

I would guess there is a problem with quotes in the file, so R thinks 
that line is a quoted string.

Set quote="" to disable recognition of quotes.  See ?read.table.

Duncan Murdoch