[Rd] read.table with ":" in column names (PR#8511)

[Roger Bivand]

On Fri, 20 Jan 2006 peverlorenvanthemaat at amc.uva.nl wrote:

> Full_Name: emiel ver loren
> Version: 2.2.0
> OS: Windows XP
> Submission from: (NULL) (145.117.31.248)
> 
> 
> Dear R-community and developers,
> 
> I have been trying to read in a tab delimeted file where the column names and
> the row names are of the form "GO:0000051" (gene ontology IDs). When using:
> 
> > gomat<-read.table("test.txt")
> > colnames(gomat)[1]
> [1] "GO.0000051"
> > rownames(gomat)[1]
> [1] "GO:0000002"
> 
> Which means that ":" is transformed into a "." !! This seems like Excel when it
> is trying to guess what I am really ment (and turning 1/1/1 into 1-1-2001).

Wrong. 

?read.table says with reference to the check.names = TRUE argument that:

"check.names: logical.  If 'TRUE' then the names of the variables in the
          data frame are checked to ensure that they are syntactically
          valid variable names.  If necessary they are adjusted (by
          'make.names') so that they are, and also to ensure that there
          are no duplicates."

> make.names("GO:0000051")
[1] "GO.0000051"

You can use "GO:0000051" as a column name if quoted, otherwise ":" is an 
operator, so the default value of the check.names argument is sound.

If you "ment" to do what you say, you should have set check.names=FALSE.

> 
> Furthermore, I found the following quite strange as well:
> 
> > gomat2<-read.delim2("test.txt",header=FALSE)
> > gomat2[1,1:2]
>           V1         V2
> 1 GO:0000051 GO:0000280
> >  as.character(gomat2[1,1:2])
> [1] "8" "2"
> > as.character(gomat2[1,1])
> [1] "GO:0000051"
> 
> I have found a way to work around it, but I am wandering what's happening....
> 
> The tab-delimited file look like:
> 
> GO:0000051	GO:0000280	GO:0000740	
> GO:0000002	0	0	0
> GO:0000004	0	0	0
> GO:0000012	0	0	0
> GO:0000014	0	0	0
> GO:0000015	0	0	0
> GO:0000018	0	0	0
> GO:0000019	0	0	0
> 
> Thanks for helping, and 
> 
> Emiel
> 
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> 

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no