toComplex             package: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)

