BioMedR (version 1.2.1)

extrDNAIncDiv: The Increment Of Diversity Descriptors

Description

The Increment Of Diversity Descriptors

Usage

extrDNAIncDiv(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

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

Details

This function calculates the The Basic Kmer Descriptor

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 extrDNAkmer

Examples

# NOT RUN {
 
pos = readFASTA(system.file('dnaseq/pos.fasta', package = 'BioMedR'))
neg = readFASTA(system.file('dnaseq/neg.fasta', package = 'BioMedR'))
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrDNAIncDiv(k = 6, x, pos, neg)
# }