extrPseDNC {rDNAse} | R Documentation |
The Pseudo Dinucleotide Composition Descriptor
Description
The Pseudo Dinucleotide Composition Descriptor
Usage
extrPseDNC(x, lambda = 3, w = 0.05, normalize = FALSE,
customprops = NULL)
Arguments
x |
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. |
w |
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. |
Details
This function calculates the pseudo dinucleotide composition Descriptor
Value
A vector
Note
if the user defined physicochemical indices have not been normalized, it should be normalized.
Author(s)
Min-feng Zhu <wind2zhu@163.com>
References
Chen W, Feng P M, Lin H, et al. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic acids research, 2013: gks1450.
See Also
See extrPseKNC
Examples
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrPseDNC(x)