Dear all,
Is there an efficient way in R to construct all strings from 4 bases (ATCG).
If we want a length L string, there are 4 ^ L possible strings of such.
e . g with L = 2 we have AA, AT, AC, AG, .. GC, GA, GT, GG as many as
4 ^ 2 = 16 strings,
with L = 3 we have as many as 4 ^ 3 = 64
Gundala
f - function(n){expand.grid(rep(list(seq_len(4)),n))}
HTH
Robin
Gundala Viswanath wrote:
Dear all,
Is there an efficient way in R to construct all strings from 4 bases (ATCG).
If we want a length L string, there are 4 ^ L possible strings of such.
e . g with L = 2 we have
Dear Ivar,
How can I extend the limit of n size?
When I tried this function with n= 15, it fails:
f - function(bases, n){apply(expand.grid(rep(list(bases),n)), 1, paste,
collapse=)}
f(c(A, T, C, G), 15)
Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
cannot allocate
Gundala Viswanath wrote:
Dear Ivar,
How can I extend the limit of n size?
When I tried this function with n= 15, it fails:
f - function(bases, n){apply(expand.grid(rep(list(bases),n)), 1, paste,
collapse=)}
f(c(A, T, C, G), 15)
Error in rep.int(rep.int(seq_len(nx),
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