R help - Jan 2009 - Converting Numerical Matrix to List of Strings

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"


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

try this:
> mapping <- c('0'='a', '1'='c',
'2'='g', '3'='t')
> x <- matrix(sample(0:3, 30, TRUE), ncol=3)
> x
      [,1] [,2] [,3]
 [1,]    3    1    1
 [2,]    1    3    2
 [3,]    1    1    1
 [4,]    1    1    1
 [5,]    2    1    3
 [6,]    1    3    0
 [7,]    1    3    2
 [8,]    3    1    0
 [9,]    0    3    0
[10,]    3    3    0
> apply(x, 1, function(z){
+     paste(mapping[as.character(z)], collapse='')
+ })
 [1] "tcc" "ctg" "ccc" "ccc"
"gct" "cta" "ctg" "tca" "ata"
"tta"
>
>

On Sun, Jan 11, 2009 at 10:38 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"
>
>
> 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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

one way is the following:

mat <- matrix(sample(0:3, 12, TRUE), 4, 3)
strg <- c("a", "c", "g", "t")

out <- strg[mat + 1]
dim(out) <- dim(mat)
apply(out, 1, paste, collapse = "")


I hope it helps.

Best,
Dimitris


Gundala Viswanath 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"
> 
> 
> 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
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus Medical Center

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