1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
|
##############################################################################
#
# 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(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 ) )
}
|
