Hi Gina,
On Thu, Jul 8, 2010 at 6:33 AM, Gina Liao <yi...@hotmail.com> wrote:
>
> Dear all,
> Hi, I have the problems about converting the matrix to adjacency
> matrix.Here's my example,
> a b c d e
> fa 1.0000000 0.4048823682 0.1228531 0.49046991 0.4945158868
> 0.307443317b 0.4048824 1.0000000000 0.4367475 0.96949219 0.0007378596
> 0.560747765c 0.1228531 0.4367474719 1.0000000 0.40037341 0.3157538204
> 0.428183667d 0.4904699 0.9694921891 0.4003734 1.00000000 0.0661313658
> 0.575606129e 0.4945159 0.0007378596 0.3157538 0.06613137 1.0000000000
> 0.001076251f 0.3074433 0.5607477645 0.4281837 0.57560613 0.0010762514
> 1.000000000
> and my threshold value is 0.4763, which means any value above it is "1" and
> any values below it is "0".
> so my adjacency matrix should be like this,
> a b c d e fa 1 0 0 1 1 0b 0 1 0 1 0 1c
> 0 0 1 0 0 0d 1 1 0 1 0 1e 1 0 0 0 1 0f
> 0 1 0 1 0 1
>
> I'd like to ask how to convert the matrix to adjacency matrix.
> Thanks!!!
Just a note for future postings: use dput (?dput) to get your matrix
into a "pastable" format that we can use to copy into a working R
session and provide code.
I'll just make own random matrix for now that I'll turn into an
adjacency matrix:
R> set.seed(123)
R> real <- matrix(runif(30, 0, 1), nrow=6)
R> colnames(real) <- c('a', 'b', 'c', 'd', 'e')
(oops that has one less column than you)
Now I can use "ifelse" to convert to an adjacency matrix
R> adj <- ifelse(real > 0.4763, 1, 0)
R> adj
a b c d e
[1,] 0 1 1 0 1
[2,] 1 1 1 1 1
[3,] 0 1 0 1 1
[4,] 1 0 1 1 1
[5,] 1 1 0 1 0
[6,] 0 0 0 1 0
The "ifelse" call could have been broken down into several steps. To
make it more clear:
Set up an "empty" adj matrix to fill w/ ones where appropriate
R> adj2 <- matrix(0, nrow=nrow(real), ncol=ncol(real))
R> colnames(adj2) <- colnames(real)
Now fill with ones:
R> adj2[real > 0.4763] <- 1
R> all(adj == adj2)
[1] TRUE
Also works.
And just to give you an idea of how to use dput:
R> dput(adj)
structure(c(1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1,
1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1), .Dim = c(6L, 5L), .Dimnames = list(
NULL, c("a", "b", "c", "d", "e")))
Hope that helps.
--
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
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