R help - Jul 2009 - Cross-validating two matrices

Hello,

I am trying to help a colleague with an R problem (see below) to whit  
I can only generate a very inelegant solution. Any advice would be  
welcome.

Thanks,
Brian

If you have two matrices, say a species by trait matrix (Matrix 1  
below) and a plot by species matrix (Matrix 2 below), is there a  
straightforward way to prune one matrix so that the species list  
matches those in a second matrix? Ideally, I need to prune both  
matrices so that they include only the species found in both. In this  
case, the two matrices would therefore include only sp1,sp4,sp5.

Thank you so much for any suggestions!

E.g.:
Matrix 1:
	Trait1
sp1 1.0
sp2 1.2
sp4 3.1
sp5 4.0
sp7 4.5

Matrix 2
		sp1	sp3 sp4 sp5 sp6
plot1	1	2	5	1	0
plot2	3	0	1	2	5	
plot3	1	1	2	3	1
plot4	0	1	2	1	0


Brian C. McCarthy, Ph.D.
Professor of Forest Ecology
Dept. of Environmental & Plant Biology
317 Porter Hall
Ohio University
Athens, OH  45701-2979  USA

T: 740-593-1615
F: 740-593-1130
E: mccarthy at ohio.edu
W:
http://www.plantbio.ohiou.edu/index.php/directory/faculty_page/brian_mccarthy/

Hi,

On Jul 27, 2009, at 3:29 PM, Brian McCarthy wrote:
> Hello,
>
> I am trying to help a colleague with an R problem (see below) to  
> whit I can only generate a very inelegant solution. Any advice would  
> be welcome.
>
> Thanks,
> Brian
>
> If you have two matrices, say a species by trait matrix (Matrix 1  
> below) and a plot by species matrix (Matrix 2 below), is there a  
> straightforward way to prune one matrix so that the species list  
> matches those in a second matrix? Ideally, I need to prune both  
> matrices so that they include only the species found in both. In  
> this case, the two matrices would therefore include only sp1,sp4,sp5.
>
> Thank you so much for any suggestions!
>
> E.g.:
> Matrix 1:
> 	Trait1
> sp1 1.0
> sp2 1.2
> sp4 3.1
> sp5 4.0
> sp7 4.5
>
> Matrix 2
> 		sp1	sp3 sp4 sp5 sp6
> plot1	1	2	5	1	0
> plot2	3	0	1	2	5	
> plot3	1	1	2	3	1
> plot4	0	1	2	1	0
keep <- intersect(rownames(matrix1), colnames(matrix2))
m1 <- matrix1[keep,]
m2 <- matrix2[,keep]

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact