.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) <mschwartz at 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 at 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