extrDNATACC: The Trinucleotide-based Auto-cross Covariance Descriptor

Description

The Trinucleotide-based Auto-cross Covariance Descriptor

Usage

extrDNATACC(x, index = c("Dnase I", "Nucleosome"), nlag = 2,
  normaliztion = FALSE, customprops = NULL, allprop = FALSE)

Arguments

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

index

the physicochemical indices, it should be a list and there are 12 different physicochemical indices (Table 2), 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 12 physicochemical indices will be employed to generate the feature vector. Its default value is False.

Value

A vector

Details

This function calculates the trinucleotide-based auto-cross covariance descriptor

Examples

Run this code

# NOT RUN {
 
x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrDNATACC(x)

# }