Turning a DNA sequence into a vector of complex numbers

Description

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

Usage

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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. Pag├Ęs

See Also

DNAString

Examples

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  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)

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