Thanks, Tao, I will try to do it.
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 [[alternative HTML version deleted]] ______________________________________________ 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.
