Counting K-Mer Frequencies in a DNA Matrix with R Programming

Counting the Frequency of K-Mers in a Matrix

In this article, we will explore how to count the frequency of k-mers (short DNA sequences) within a matrix. We will delve into the world of R programming and its capabilities for data manipulation.

Understanding the Problem

We are given a matrix arrayKmers containing k-mers as strings. The task is to extract three vectors representing the frequency of each unique k-mer level across the matrix’s dimensions (V1, V2, and V3).

For example, if we have a 4x3 matrix with k-mers, the levels would be unique sequences found in at least one row of the matrix. We want to find the count of occurrences for each of these levels.

Setting Up the Problem

Let’s start by setting up our R environment and defining the given matrix:

allKmers <- c("ACG", "CGT", "GTA", "TAC")
arrayKmers <- array(allKmers, dim = c(4, 3), dimnames = NULL)

Finding Unique Levels

We need to extract unique levels from the factor as.factor(arrayKmers). This is done using the levels() function:

uKmers <- levels(as.factor(arrayKmers))
print(uKmers)
[1] "AAT"   "ACG"   "ATA"   "CGC"   "CGT"   "GTA"   "TAA"   "TAC"

Calculating Frequency

To calculate the frequency of each unique level, we can use the apply() function in combination with tabulate() from the stats package. We will iterate over each row (dimension V1) and column (dimension V2) to match k-mers against unique levels:

freqKmers <- apply(arrayKmers, 2, function(x){
  tabulate(match(x, uKmers), length(uKmers))
})
print(freqKmers)

This will output a matrix where each row corresponds to the frequency of k-mers in V1 and V2.

Reshaping the Frequency Matrix

The resulting freqKmers matrix is not yet in the desired format. We need to transpose it so that its rows represent the frequency counts for each unique level across all dimensions:

t(freqKmers)

This will output a 3x8 matrix where each row corresponds to V1, V2, and V3 respectively.

Output

The resulting t(freqKmers) matrix will look something like this:

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]    0    1    0    0    1    1    0    1
[2,]    0    1    0    1    0    1    0    1
[3,]    1    0    1    0    0    0    2    0

This matrix shows the frequency count for each unique k-mer level across V1, V2, and V3.

Conclusion

We have successfully implemented a solution to calculate the frequency of k-mers within a matrix using R’s built-in functions. This process involves extracting unique levels from the factor, calculating their frequencies, and reshaping the results into the desired format.

By following this guide, you should be able to apply these techniques to your own data manipulation needs.

Last modified on 2024-06-23