[R] Converting Numerical Matrix to List of Strings

[Douglas Bates]

On Sun, Jan 11, 2009 at 9:38 AM, Gundala Viswanath <gundalav at gmail.com> wrote:
> Hi all,
>
> Given a matrix:
>
>> mat
>
>    [,1] [,2] [,3]
> [1,]    0    0    0
> [2,]    3    3    3
> [3,]    1    1    1
> [4,]    2    1    1

> How can I convert it to a list of strings:

>> desired_output
> [1] "aaa" "ttt" "ccc" "gcc"

Are you looking for a general solution or do you want something
specific for these 64 potential codon-like patterns?  If you just want
the patterns corresponding to all possible triplets of A, C, G, T then

colSums(4^(0:2) * t(mat)) + 1

gives you a set of indices between 1 and 64.  Then you need to create
the 64 possible patterns.  Here is one way

> bases <- factor(c("A","C","G","T"))
> head(patterns <- do.call(paste, expand.grid(bases, bases, bases)))
[1] "A A A" "C A A" "G A A" "T A A" "A C A" "C C A"
> (mat <- matrix(c(0,3,1,2,0,3,1,1,0,3,1,1), ncol = 3))
     [,1] [,2] [,3]
[1,]    0    0    0
[2,]    3    3    3
[3,]    1    1    1
[4,]    2    1    1
> colSums(4^(0:2) * t(mat)) + 1
[1]  1 64 22 23
> patterns[colSums(4^(0:2) * t(mat)) + 1]
[1] "A A A" "T T T" "C C C" "G C C"

We will leave the elimination of the blanks in the patterns as an
exercise for the reader.

>
> In principle:
>
> 1. Number of Column in matrix = length of string (= 3)
> 2. Number of Row in matrix = length of vector ( = 4).
> 3. Character "a" encode as "0",
>  "c" -> "1",
>  "g" -> "2",
>  "t" -> "3"
>
>
> Length of strings are assumed to be uniform within the vector,
> and it can be greater than 3 (up to 40 characters).
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
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