[R] Pairwise correlation
R. Michael Weylandt
michael.weylandt at gmail.com
Thu Nov 17 14:51:15 CET 2011
On Wed, Nov 16, 2011 at 11:22 PM, muzz56 <musahass at gmail.com> wrote:
> Thanks to everyone who replied to my post, I finally got it to work. I am
> however not sure how well it worked since it run so quickly, but seems like
> I have a 2000 x 2000 data set.
Behold the great and mighty power that is R! Don't worry -- on a
decent machine the correlation of a 2k x 2k data set should be pretty
fast. (It's about 9 seconds on my old-ish laptop with a bunch of other
> My followup questions would be, how do I get
> only pairs with say a certain pearson correlation value additionally it
> seems like my output didn't retain the headers but instead replaced them
> with numbers making it hard to know which gene pairs correlate.
This is a little worrisome: R carries column names through cor() so
this would suggest you weren't using them. Were your headers listed as
part of your data (instead of being names)? If so, they would have
been taken as numbers.
Take a look at dimnames(NAMEOFDATA) -- if your headers aren't there,
then they are being treated as data instead of numbers. If they are,
can you provide some reproducible code and we can debug more fully.
The easiest way to send data is to use the dput() function to get a
copy-pasteable plain text representation. It would also be great if
you could restrict it to a subset of your data rather than the full 4M
data points, but if that's hard to do, don't worry.
You should have expected behavior like
X <- matrix(1:9,3)
colnames(X) <- c("A","B","C")
cor(X) # Prints with labels
> On 16 November 2011 17:11, Nordlund, Dan (DSHS/RDA) [via R] <
> ml-node+s789695n4078114h81 at n4.nabble.com> wrote:
>> > -----Original Message-----
>> > From: [hidden email]<http://user/SendEmail.jtp?type=node&node=4078114&i=0>[mailto:
>> r-help-bounces at r-
>> > project.org] On Behalf Of muzz56
>> > Sent: Wednesday, November 16, 2011 12:28 PM
>> > To: [hidden email]<http://user/SendEmail.jtp?type=node&node=4078114&i=1>
>> > Subject: Re: [R] Pairwise correlation
>> > Thanks Peter. I tried this after reading in the csv (read.csv) and
>> > converted the data to matrix (as.matrix). But when I tried the
>> > correlation,
>> > I keeping getting the error (x must be numeric) yet when I view the
>> > data,
>> > its numeric.
>> What does R tell you if you execute the following?
>> Just because the data looks like it is numeric when it prints doesn't mean
>> it is.
>> Daniel J. Nordlund
>> Washington State Department of Social and Health Services
>> Planning, Performance, and Accountability
>> Research and Data Analysis Division
>> Olympia, WA 98504-5204
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