Kmer-package: K-mer calculation using C++ with Rcpp.
In Kmer: Computes a matrix of K-mer counts.

Description Details Author(s) References See Also Examples

Calculates K-mers from string vectors.

No details so far.

Kristian Hovde Liland

TODO:

Please don't.

# Basic
system.time(a <- Kmer(c("AAACGTTTT","GTTT"),3,TRUE))
dim(a)
sum(a)
print(a)

# 0/1 instead of count
system.time(aR <- KmerRDP(c("AAACGTTTT","GTTT"),3,TRUE))

# Alien characters
system.time(aA <- KmerAlien(c("AAANGTTTT","GTTT"),3,TRUE))
system.time(aAR <- KmerAlienRDP(c("AAANGTTTT","GTTT"),3,TRUE))

# Count for classes
system.time(b <- Kmer_classes(c("AAACGTTTT","GTTT"),3,TRUE,c("Fish","Coconut")))
print(b)