Re: [R] .gct file

From: mark salsburg <mark.salsburg_at_gmail.com>
Date: Wed 20 Jul 2005 - 03:52:55 EST

This is all extremely helpful.

The data turns out is a little atypical, the columns are tab-delemited except for the description columns

DATA1.gct looks like this

#1.2
23 3423
NAME DESCRIPTION VALUE
gene1 "a protein inducer" 1123

.....          .................     ......

How do I get R to read the data as tab delemited, but read in the 2nd coloumn as one value based on the quotation marks..

thanks..

On 7/19/05, Marc Schwartz (via MN) <mschwartz@mn.rr.com> wrote:
> On Tue, 2005-07-19 at 13:16 -0400, mark salsburg wrote:
> > ok so the gct file looks like this:
> >
> > #1.2 (version number)
> > 7283 19 (matrix size)
> > Name Description Values
> > .... ....... ......
> >
> > How can I tell R to disregard the first two lines and start reading
> > the 3rd line in this gct file. I would just delete them, but I do not
> > know how to open a gct. file
> >
> > thank you
> >
> > On 7/19/05, Duncan Murdoch <murdoch@stats.uwo.ca> wrote:
> > > On 7/19/2005 12:10 PM, mark salsburg wrote:
> > > > I have two files to compare, one is a regular txt file that I can read
> > > > in no prob.
> > > >
> > > > The other is a .gct file (How do I read in this one?)
> > > >
> > > > I tried a simple
> > > >
> > > > read.table("data.gct", header = T)
> > > >
> > > > How do you suggest reading in this file??
> > > >
> > >
> > > .gct is not a standard filename extension. You need to know what is in
> > > that file. Where did you get it? What program created it?
> > >
> > > Chances are the easiest thing to do is to get the program that created
> > > it to export in a well known format, e.g. .csv.
> > >
> > > Duncan Murdoch
>
>
> The above would be consistent with the info in my reply.
>
> I guess if the format is consistent, as per Mark's example above, you
> can use:
>
> read.table("data.gct", skip = 2, header = TRUE)
>
> which will start by skipping the first two lines and then reading in the
> header row and then the data.
>
> See ?read.table
>
> HTH,
>
> Marc Schwartz
>
>
>



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