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
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
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.
__
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
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,
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
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,
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
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
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
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
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
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
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
14 matches
Mail list logo
