Thanks, Tao, I will try to do it.


On Tue, May 25, 2010 at 10:13 AM, Shi, Tao <shidaxia@yahoo.com> wrote:

> Changbin,
>
> It looks you're trying to read in a gene annotation file and usually it has
> many strange characters, e.g. "#", "&", ....  (as other people also
> suggest).   I encounter this all the time.  So try to be very thorough about
> your search (the first place I'll look for is the line where R stop reading.
>  See if any thing strange there.)
>
> Also, changing "read.table" to "read.delim" often works.
>
> ...Tao
>
>
>
>
>
> ----- Original Message ----
> > From: Changbin Du <changbind@gmail.com>
> > To: David Winsemius <dwinsemius@comcast.net>
> > Cc: r-help@r-project.org
> > Sent: Tue, May 25, 2010 9:12:58 AM
> > Subject: Re: [R] R eat my data
> >
> > 644727344    ABC-2 type transporter    ABC-2 type
> > transporter
> 644727345    conserved hypothetical protein
> >   conserved hypothetical
> protein
>
> Here is the last two lines of
> > the file id_name_gh5.txt.
>
>
>
> On Tue, May 25, 2010 at 8:57 AM, David
> > Winsemius <
> > href="mailto:dwinsemius@comcast.net">dwinsemius@comcast.net>wrote:
>
> >
> >
> > On May 25, 2010, at 11:42 AM, Changbin Du wrote:
> >
> >  HI, Dear
> > R community,
> >>
> >> My original file has 1932 lines, but when I
> > read into R, it changed to
> >> 1068
> >> lines, how
> > comes?
> >>
> >
> > We are being asked to investigate this quest,
> > how?
> >
> > Have you looked at the last line to see if it looks like
> > gene_name?
> >
> > Isn't this isomorphic to genetics questions? What
> > sort of mutation is it?
> > Deletion? Abnormal stop codon? Figure out where
> > the transcription process
> > went wrong.  This sort of analysis would
> > appear to be right up the alley of
> > someone doing
> > genetics.
> >
> >
> >
> >>
> >> cdu@nuuk:~/operon$ wc
> > -l id_name_gh5.txt
> >> 1932
> > id_name_gh5.txt
> >>
> >>
> >>
> > gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt",
> > sep="\t",
> >>>
> >> skip=0, header=F,
> > fill=T)
> >>
> >>> dim(gene_name)
> >>>
> >>
> > [1] 1068    3
> >>
> >>
> >>
> > --
> >>
> >
> >
> > David Winsemius, MD
> > West
> > Hartford, CT
> >
> >
>
>
> --
> >
> Sincerely,
> Changbin
> --
>
>     [[alternative HTML
> > version deleted]]
>
> ______________________________________________
>
> > ymailto="mailto:R-help@r-project.org"
> > href="mailto:R-help@r-project.org">R-help@r-project.org mailing list
>
> > href="https://stat.ethz.ch/mailman/listinfo/r-help" target=_blank
> > >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.
>
>
>
>


-- 
Sincerely,
Changbin
--

Changbin Du
DOE Joint Genome Institute
Bldg 400 Rm 457
2800 Mitchell Dr
Walnut Creet, CA 94598
Phone: 925-927-2856

	[[alternative HTML version deleted]]

