BioMedR (version 1.2.1)

extrDNAkmer: The Basic Kmer Descriptor

Description

The Basic Kmer Descriptor

Usage

extrDNAkmer(x, k = 2, upto = FALSE, normalize = FALSE,
  reverse = FALSE)

Arguments

x

the input data, which should be a list or file type.

k

the k value of kmer, it should be an integer larger than 0.

upto

generate all the kmers: 1mer, 2mer, ..., kmer. The output feature vector is the combination of all these kmers. The default value of this parameter is False.

normalize

with this option, the final feature vector will be normalized based on the total occurrences of all kmers. Therefore, the elements in the feature vectors represent the frequencies of kmers. The default value of this parameter is False.

reverse

make reverse complements into a single feature, The default value of this parameter is False. if reverse is True, this method returns the reverse compliment kmer feature vector.

Value

A vector

Details

This function calculates the basic kmer descriptor

References

Noble W S, Kuehn S, Thurman R, et al. Predicting the in vivo signature of human gene regulatory sequences. Bioinformatics, 2005, 21 Suppl 1, i338-343. Lee D, Karchin R, Beer M A. Discriminative prediction of mammalian enhancers from DNA sequence. Genome research. 2005, 21, 2167-2180.

See Also

See make_kmer_index

Examples

# NOT RUN {
 
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrDNAkmer(x)

# }