extrDAC {rDNAse} | R Documentation |
The Dinucleotide-based Auto Covariance Descriptor
Description
The Dinucleotide-based Auto Covariance Descriptor
Usage
extrDAC(x, index = c("Twist", "Tilt"), nlag = 2, normaliztion = FALSE,
customprops = NULL, allprop = FALSE)
Arguments
x |
the input data, which should be a list or file type. |
index |
the physicochemical indices, it should be a list and there are 38 different physicochemical indices (Table 1), which the users can choose. |
nlag |
an integer larger than or equal to 0 and less than or equal to L-2 (L means the length of the shortest DNA sequence in the dataset). It represents the distance between two dinucleotides. |
normaliztion |
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. |
allprop |
all the 38 physicochemical indices will be employed to generate the feature vector. Its default value is False. |
Details
This function calculates the dinucleotide-based auto covariance 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
Dong Q, Zhou S, Guan J. A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation. Bioinformatics, 2009, 25(20): 2655-2662.
See Also
Examples
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrDAC(x)