[R] Unexpected behaviour in reading genomic coordinate files of R-2.7.0

[Margherita]

Great R people,

I have noticed a strange behaviour in read.delim() and friends in the R 
2.7.0 version. I will describe you the problem and also the solution I 
already found, just to be sure it is an expected behaviour and also to 
tell people, who may experience the same difficulty, a way to overcome it.
And also to see if it is a proper behaviour or maybe a correction is needed.

Here is the problem:
I have some genomic coordinates files (bed files, a standard format, for 
example) containing a column (Strand) in which there is either a "+" or 
a "-".
In R-2.6.2patched (and every past version I have used) I never had 
problems in reading them in, as for example:
 > a <- read.table("coords.bed", skip=1)
 > disp(a)
class  data.frame
dimensions are  38650 6
first rows:
    V1        V2        V3    V4 V5 V6
1 chr1 100088396 100088446  seq1  0  +
2 chr1 100088764 100088814  seq2  0  -

If I do exactly the same command on the same file in R-2.7.0 the result 
I obtain is:
 > a <- read.table("coords.bed", skip=1)
 > disp(a)
class  data.frame
dimensions are  38650 6
first rows:
    V1        V2        V3    V4 V5 V6
1 chr1 100088396 100088446  seq1  0  0
2 chr1 100088764 100088814  seq2  0  0

and I completely loose the strand information, they are all zeros! I 
have also tried to put quotes around "+" and "-" in the file before 
reading it, to set in read.table() call stringsAsFactors=FALSE, to set 
"encoding" to a few different alternatives, but the result was always 
the same: they are all transformed in 0.

Then I tried scan() and I saw it was reading the character "+" properly:
 > scan("coords.bed",  skip=1, nlines=1, what="ch")
Read 6 items
[1] "chr1"         "100088396"    "100088446.00" "seq1" "0"          
[6] "+"  

...my conclusion is that the lone "+" or "-" are not taken as 
"characters" in the data frame creation step, they are taken as 
"numeric" but, being without numbers are all converted to 0.
Is it correct if this behaviour happens also if they are surrounded by 
quotes?

Anyway, my temporary solution (which works without the need of changing 
the files) is:
a <- read.table("coords.bed", skip=1, colClasses=c("character", 
"numeric", "numeric", "character", "numeric", "character"))
 > a[1:2,]
    V1        V2        V3    V4 V5 V6
1 chr1 100088396 100088446 seq1  0  +
2 chr1 100088764 100088814 seq2  0  -

Another way to avoid loosing strand information was to manually 
substitute an "R" to "-" and an "F" to "+" in the file before reading it 
in R. But it is much more cumbersome since the use of + and - is, for 
example, a standard format in bed files accepted and generated by the 
Genome Browser and other genome sites.

Please let me know what do you think. Ps. I saw this first in the Fedora 
version (rpm automatically updated), but it is reproduced also in the 
Windows version.

Thank you all people for your work and for making R the wonderful tool 
it is!

Cheers,

Margherita

-- 
 --
 -----------------------------------------------------------------------------------
 Margherita Mutarelli, PhD 
Seconda Universita' di Napoli
Dipartimento di Patologia Generale
 via L. De Crecchio, 7
 80138 Napoli - Italy
 Tel/Fax. +39.081.5665802