extrPseDNC: The Pseudo Dinucleotide Composition Descriptor

Description

The Pseudo Dinucleotide Composition Descriptor

Usage

extrPseDNC(x, lambda = 3, w = 0.05, normalize = FALSE, customprops = NULL)

Arguments

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

lambda

an integer larger than or equal to 0 and less than or equal to L-2 (L means the length of the shortest sequence in the dataset). It represents the highest counted rank (or tier) of the correlation along a DNA sequence. Its default value is 3.

the weight factor ranged from 0 to 1. Its default value is 0.05.

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.

customprops

the users can use their own indices to generate the feature vector. It should be a dict, the key is dinucleotide (string), and its corresponding value is a list type.

Value

A vector

Details

This function calculates the pseudo dinucleotide composition Descriptor

References

Chen W, Feng P M, Lin H, et al. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic acids research, 2013: gks1450.

Examples

Run this code

x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrPseDNC(x)

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