extrDNAIncDiv: The Increment Of Diversity Descriptors

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/602-extractDNAIncDiv.R

Description

The Increment Of Diversity Descriptors

Usage

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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

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 extrDNAkmer

Examples

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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)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.