R help - Dec 2009 - selective subsetting of a correlation matrix

Dear All,
I have a correlation matrix say 'M' (4000x4000) for 4000 genes and I
want to
subset it to 'N' (190x190) for 190 genes.
The list of those 190 genes are in variable 't'. So the idea is to read
the
names of genes from variable 't' and subset the matrix M accordingly.
Any thoughts are welcome!

Best
Lee

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On 12/04/2009 02:18 PM, Lee William wrote:
>
> Dear All,
> I have a correlation matrix say 'M' (4000x4000) for 4000 genes and
I want to
> subset it to 'N' (190x190) for 190 genes.
> The list of those 190 genes are in variable 't'. So the idea is to
read the
> names of genes from variable 't' and subset the matrix M
accordingly.
> Any thoughts are welcome!
>
> Best
> Lee
Hi,

Assuming the correlation matrix has dimnames, you can do :

x[ rownames(x) %in% t, colnames(x) %in% t ]

Here is a reproducible example, please make sure you provide one next time.

x <- expand.grid( x1 = 1:2, x2 = 1:2, x3 = 1:2, x4 = 1:2 )
y <- cor( x )
t <- c("x1", "x2")
y[ rownames(y) %in% t, colnames(y) %in% t ]

Romain


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Will something like this work for you:
> x <- matrix(1:100,10)
> dimnames(x) <- list(letters[1:10], LETTERS[1:10])
> x
   A  B  C  D  E  F  G  H  I   J
a  1 11 21 31 41 51 61 71 81  91
b  2 12 22 32 42 52 62 72 82  92
c  3 13 23 33 43 53 63 73 83  93
d  4 14 24 34 44 54 64 74 84  94
e  5 15 25 35 45 55 65 75 85  95
f  6 16 26 36 46 56 66 76 86  96
g  7 17 27 37 47 57 67 77 87  97
h  8 18 28 38 48 58 68 78 88  98
i  9 19 29 39 49 59 69 79 89  99
j 10 20 30 40 50 60 70 80 90 100
> x[c('c','g','j'),
c("B","E","I")]
   B  E  I
c 13 43 83
g 17 47 87
j 20 50 90
>

On Fri, Dec 4, 2009 at 8:18 AM, Lee William <leeonweb@gmail.com> wrote:
> Dear All,
> I have a correlation matrix say 'M' (4000x4000) for 4000 genes and
I want
> to
> subset it to 'N' (190x190) for 190 genes.
> The list of those 190 genes are in variable 't'. So the idea is to
read the
> names of genes from variable 't' and subset the matrix M
accordingly.
> Any thoughts are welcome!
>
> Best
> Lee
>
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>
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>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>


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What is the problem that you are trying to solve?

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