make_idkmer_vec {rDNAse} | R Documentation |
The Increment Of Diversity Descriptors
Description
The Increment Of Diversity Descriptors
Usage
make_idkmer_vec(k = 6, x, pos, neg, upto = TRUE)
Arguments
k |
the k value of kmer, it should be an integer larger than 0,the default value is 6. |
x |
the input data, which should be a list or file type. |
pos |
the positive source data, which should be a or type. |
neg |
the negative source data, which should be or type. |
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 True |
Details
This function calculates the The Basic Kmer Descriptor
Value
if upto is True, A length k * 2
named vector, k
is the k value of kmer;
if upto is False, A length 2 named vector
Author(s)
Min-feng Zhu <wind2zhu@163.com>
References
Chen W, Luo L, Zhang L. The organization of nucleosomes around splice sites. Nucleic acids research, 2010, 38(9): 2788-2798. Liu G, Liu J, Cui X, et al. Sequence-dependent prediction of recombination hotspots in Saccharomyces cerevisiae. Journal of theoretical biology, 2012, 293: 49-54.
See Also
See kmer
Examples
pos = readFASTA(system.file('dnaseq/pos.fasta', package = 'rDNAse'))
neg = readFASTA(system.file('dnaseq/neg.fasta', package = 'rDNAse'))
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
make_idkmer_vec(k = 6, x, pos, neg)