R/s2n.R

In seqinr: Biological Sequences Retrieval and Analysis

##############################################################################
#
# simple numerical encoding of a DNA sequence that by default
# is independent of locale.
#
##############################################################################

s2n <- function(seq, levels = s2c("acgt"), base4 = TRUE, forceToLower = TRUE)
{
    #
    # Check that sequence is a vector of chars:
    #
    if(!is.na(seq[1])){
        if(nchar(seq[1]) > 1) stop("sequence is not a vector of chars")
    }
    #
    # Force to lower-case letters if requested:
    #
    if(forceToLower) seq <- tolower(seq)
    
    if( base4 )
        unclass(factor(seq, levels = levels ) ) - 1
    else
        unclass(factor(seq, levels = levels ) )
}