gene_name<-read.delim("/home/cdu/operon/id_name_gh5.txt", sep="\t", skip=0,
header=F, fill=T)
> dim(gene_name)
[1] 1932 3
Thanks, Tao! Now you see, read.delim works!
Thanks all for your imputs! I really appreciated!
On Tue, May 25, 2010 at 10:13 AM, Shi, Tao <shida...@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 <changb...@gmail.com>
> > To: David Winsemius <dwinsem...@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:dwinsem...@comcast.net";>dwinsem...@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.
> >
> >
> >
> >>
> >> c...@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
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