How to calculate dinucleotide A/T patterns in a given human reference genome region?

Question

[Ashley]

library("Biostrings")

I want to calculate the probability of di-nucleotide AA, TT, AT, and TA in each 2 location.

My DNA sequence is as follows:

DNA.set
  A DNAStringSet instance of length 5
    width seq                                                              names               
[1]    20 TCCGTATTGGAAAGCTCGTC                                             SEQ-1
[2]    20 TTAGACCACTCCGCATGTAG                                             SEQ-2
[3]    20 CTGTGGTACGGCTCAAACGG                                             SEQ-3
[4]    20 CTCCCGCCTATCTCCCTTCT                                             SEQ-4
[5]    20 TCGCCTAGAAAAAGTTTCCT                                             SEQ-5

I want to obtain the result as follows:

AA=0,0,0,0,1/5,2/5,0,1/5,0,0
TT=1/5,0,0,0,0,0,0,1/5,1/5,0
AT=0,0,0,0,0,0,0,0,1/5,0,0
TA=0,0,1/5,1/5,1/5,0,0,0,0,0

Any help would be great appreciate.

[morovatunc]

dinucleotideFrequency function of biostrings could give those 2mers. than you can take the subset of your desired ones.

[Ashley]

> dinucleotideFrequency(DNA.set)
     AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT
[1,]  2  0  1  1  0  1  2  1  1  1  1  2  1  3  1  1
[2,]  0  2  2  1  2  2  1  1  1  1  0  1  2  1  1  1
[3,]  2  2  0  0  1  0  2  2  0  1  3  2  1  1  2  0
[4,]  0  0  0  1  0  5  1  5  0  1  0  0  1  4  0  1
[5,]  4  0  2  0  0  2  1  2  1  1  0  1  1  2  0  2

Thanks for your reply. But I want to know the frequency or probability of A/T in each position. Not total number. So dinucleotideFrequency maybe isn't suitable for me.

[morovatunc]

consensusMatrix(dinucleotideFrequency(DNA.set)) ? maybe ?

[Ashley]

For our example,

> consensusMatrix(dinucleotideFrequency(DNA.set))
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
0    2    3    2    2    3    1    0    0    2     0     3     1     0     0     2     1
1    0    0    1    3    1    1    3    2    3     5     1     2     4     2     2     3
2    2    2    2    0    1    2    2    2    0     0     0     2     1     1     1     1
3    0    0    0    0    0    0    0    0    0     0     1     0     0     1     0     0
4    1    0    0    0    0    0    0    0    0     0     0     0     0     1     0     0
5    0    0    0    0    0    1    0    1    0     0     0     0     0     0     0     0

Thanks for your kind help. But I think the column of result should be the length(DNA.seq)/2=10, however, the column is 16. And it didn't show which column represents for AA, AT, TA and TT. I am the newcomer of bioinformatics, could you help me figure it out? Thank you so much. With my best wishes.

I think the number of column is always the 16. For another example,

> dna2
  A DNAStringSet instance of length 3
    width seq                                                              names               
[1]     4 ACGT                                                             seq1
[2]     4 GTCA                                                             seq2
[3]     4 GCTA                                                             seq3
> consensusMatrix(dna2, as.prob = TRUE)
       [,1]      [,2]      [,3]      [,4]
A 0.3333333 0.0000000 0.0000000 0.6666667
C 0.0000000 0.6666667 0.3333333 0.0000000
G 0.6666667 0.0000000 0.3333333 0.0000000
T 0.0000000 0.3333333 0.3333333 0.3333333
M 0.0000000 0.0000000 0.0000000 0.0000000
R 0.0000000 0.0000000 0.0000000 0.0000000
W 0.0000000 0.0000000 0.0000000 0.0000000
S 0.0000000 0.0000000 0.0000000 0.0000000
Y 0.0000000 0.0000000 0.0000000 0.0000000
K 0.0000000 0.0000000 0.0000000 0.0000000
V 0.0000000 0.0000000 0.0000000 0.0000000
H 0.0000000 0.0000000 0.0000000 0.0000000
D 0.0000000 0.0000000 0.0000000 0.0000000
B 0.0000000 0.0000000 0.0000000 0.0000000
N 0.0000000 0.0000000 0.0000000 0.0000000
- 0.0000000 0.0000000 0.0000000 0.0000000
+ 0.0000000 0.0000000 0.0000000 0.0000000
. 0.0000000 0.0000000 0.0000000 0.0000000
> dim(consensusMatrix(dna2, as.prob = TRUE))
[1] 18  4
> consensusMatrix(dinucleotideFrequency(dna2))
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
0    3    2    3    3    2    3    2    2    3     2     3     1     2     2     3     3
1    0    1    0    0    1    0    1    1    0     1     0     2     1     1     0     0

[Ashley]

(original link: https://www.dropbox.com/s/h8de0hcc8vc193t/data.jpg?dl=0 )