R: Turning a DNA sequence into a vector of complex numbers

toComplex {Biostrings} | R Documentation

## Turning a DNA sequence into a vector of complex numbers

### Description

The `toComplex` utility function turns a DNAString object into a complex vector.

### Usage

      toComplex(x, baseValues)

### Arguments

`x` | A DNAString object.
`baseValues` | A named complex vector containing the values associated to each base e.g. `c(A=1+0i, G=0+1i, T=-1+0i, C=0-1i)`

### Value

A complex vector of the same length as `x`.

### Author(s)

H. Pages

### See Also

DNAString

### Examples

      seq <- DNAString("accacctgaccattgtcct")
      baseValues1 <- c(A=1+0i, G=0+1i, T=-1+0i, C=0-1i)
      toComplex(seq, baseValues1)

      ## GC content:
      baseValues2 <- c(A=0, C=1, G=1, T=0)
      sum(as.integer(toComplex(seq, baseValues2)))
      ## Note that there are better ways to do this (see ?alphabetFrequency)

[Package Biostrings version 2.16.9 Index]