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
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
