Re: [R] .gct file
Those wondering what gtc file stands for, might be interested in [1].
The original poster can see if the package 'ctc' [2] supports reading in
this format but I think Prof. Ripley's solution works too.
[1]http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_tutorial_fileformats.html
[2]http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ctc.html
On Wed, 2005-07-20 at 09:52 +0100, Prof Brian Ripley wrote:
> On Tue, 19 Jul 2005, Marc Schwartz (via MN) wrote:
>
> > For the TAB delimited columns, adjust the 'sep' argument to:
> >
> > read.table("data.gct", skip = 2, header = TRUE, sep = "\t")
> >
> > The 'quote' argument is by default:
> >
> > quote = "\"'"
> >
> > which should take care of the quoted strings and bring them in as a
> > single value.
> >
> > The above presumes that the header row is also TAB delimited. If not,
> > you may have to set 'skip = 3' to skip over the header row and manually
> > set the column names.
>
> Not quite. You can open a connection, skip 2 rows and read one to get the
> column names, then read the rest of the file using read.table on the open
> connection using the column names you just read.
>
> However, based on what we have been shown
>
> read.table("data.gct", skip = 2, header = TRUE)
>
> ought to work as the file looks as if it is white-space delimited (a tab
> is white space).
>
> >
> > HTH,
> >
> > Marc Schwartz
> >
> >
> > On Tue, 2005-07-19 at 13:52 -0400, mark salsburg wrote:
> >> 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) <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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
> >>>
> >>>
> >>>
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> >
>
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Re: [R] .gct file
On Tue, 19 Jul 2005, Marc Schwartz (via MN) wrote:
> For the TAB delimited columns, adjust the 'sep' argument to:
>
> read.table("data.gct", skip = 2, header = TRUE, sep = "\t")
>
> The 'quote' argument is by default:
>
> quote = "\"'"
>
> which should take care of the quoted strings and bring them in as a
> single value.
>
> The above presumes that the header row is also TAB delimited. If not,
> you may have to set 'skip = 3' to skip over the header row and manually
> set the column names.
Not quite. You can open a connection, skip 2 rows and read one to get the
column names, then read the rest of the file using read.table on the open
connection using the column names you just read.
However, based on what we have been shown
read.table("data.gct", skip = 2, header = TRUE)
ought to work as the file looks as if it is white-space delimited (a tab
is white space).
>
> HTH,
>
> Marc Schwartz
>
>
> On Tue, 2005-07-19 at 13:52 -0400, mark salsburg wrote:
>> 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) <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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
>>>
>>>
>>>
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] .gct file
On Tue, 2005-07-19 at 13:08 -0500, Marc Schwartz (via MN) wrote:
> For the TAB delimited columns, adjust the 'sep' argument to:
>
> read.table("data.gct", skip = 2, header = TRUE, sep = "\t")
>
> The 'quote' argument is by default:
>
> quote = "\"'"
>
> which should take care of the quoted strings and bring them in as a
> single value.
>
> The above presumes that the header row is also TAB delimited. If not,
> you may have to set 'skip = 3' to skip over the header row and manually
> set the column names.
One correction. If the final para applies and you need to use 'skip =
3', you would also need to leave out the 'header = TRUE' argument, which
defaults to FALSE.
Marc
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Re: [R] .gct file
On Tue, 2005-07-19 at 13:08 -0500, Marc Schwartz (via MN) wrote:
> For the TAB delimited columns, adjust the 'sep' argument to:
>
> read.table("data.gct", skip = 2, header = TRUE, sep = "\t")
>
> The 'quote' argument is by default:
>
> quote = "\"'"
>
> which should take care of the quoted strings and bring them in as a
> single value.
>
> The above presumes that the header row is also TAB delimited. If not,
> you may have to set 'skip = 3' to skip over the header row and manually
> set the column names.
One correction. If the final para applies and you need to use 'skip =
3', you would also need to leave out the 'header = TRUE' argument, which
defaults to FALSE.
Marc
__
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Re: [R] .gct file
For the TAB delimited columns, adjust the 'sep' argument to:
read.table("data.gct", skip = 2, header = TRUE, sep = "\t")
The 'quote' argument is by default:
quote = "\"'"
which should take care of the quoted strings and bring them in as a
single value.
The above presumes that the header row is also TAB delimited. If not,
you may have to set 'skip = 3' to skip over the header row and manually
set the column names.
HTH,
Marc Schwartz
On Tue, 2005-07-19 at 13:52 -0400, mark salsburg wrote:
> 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) <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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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Re: [R] .gct file
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) <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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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Re: [R] .gct file
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 <[EMAIL PROTECTED]> 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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Re: [R] .gct file
Try ?read.table or args(read.table). Might "skip=2" do what you want?
spencer graves
p.s. I routinely "readLines(File, n=11)" to see how many headers there
are AND identify the "sep" character. Then I
"quantile(count.fields(File, ...))" to see if all records have the same
number of fields. Then I call something like "read.table" with the
appropriate arguments. Then I print the first 2 or so rows of the
result to make sure I read the file correctly.
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 <[EMAIL PROTECTED]> 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
>>
>
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA
[EMAIL PROTECTED]
www.pdf.com
Tel: 408-938-4420
Fax: 408-280-7915
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Re: [R] .gct file
On 7/19/2005 1:16 PM, 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 Use skip=2. See ?read.table. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] .gct file
If it is a text file ?read.table should provide enough details to read the
file into R. Based on the file format referenced below it shouldn't be too
hard to get at the parts you want.
Randy
On 7/19/05 1:06 PM, "Marc Schwartz (via MN)" <[EMAIL PROTECTED]> wrote:
> On Tue, 2005-07-19 at 12:28 -0400, Duncan Murdoch 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
>
> A quick Google search would suggest "Gene Cluster Text" file:
>
> http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_tutorial_file
> formats.html#gct
>
> produced by Gene Pattern:
>
> http://www.broad.mit.edu/cancer/software/genepattern/
>
> If correct, I would point Mark to the Bioconductor folks for more
> information and assistance:
>
> http://www.bioconductor.org/
>
> HTH,
>
> Marc Schwartz
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
~~
Randy Johnson
Laboratory of Genomic Diversity
NCI-Frederick
Bldg 560, Rm 11-85
Frederick, MD 21702
(301)846-1304
~~
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Re: [R] .gct file
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 <[EMAIL PROTECTED]> 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
>
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Re: [R] .gct file
On Tue, 2005-07-19 at 12:28 -0400, Duncan Murdoch 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
A quick Google search would suggest "Gene Cluster Text" file:
http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_tutorial_fileformats.html#gct
produced by Gene Pattern:
http://www.broad.mit.edu/cancer/software/genepattern/
If correct, I would point Mark to the Bioconductor folks for more
information and assistance:
http://www.bioconductor.org/
HTH,
Marc Schwartz
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Re: [R] .gct file
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
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[R] .gct file
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??
thank you.
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