Description Usage Arguments Details Value Note Author(s) References See Also Examples
The Pseudo K-tupler Composition Descriptor
1 2 | extrPseKNC(x, lambda = 1, k = 3, normalize = FALSE, w = 0.5,
customprops = NULL)
|
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. |
k |
an integer larger than 0 represents the k-tuple. Its default value is 3. |
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. |
w |
the weight factor ranged from 0 to 1. Its default value is 0.05. |
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. |
This function calculates the pseudo k-tupler composition Descriptor
A vector
if the user defined physicochemical indices have not been normalized, it should be normalized.
Min-feng Zhu <wind2zhu@163.com>
Guo S H, Deng E Z, Xu L Q, et al. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinformatics, 2014: btu083.
See extrPseDNC
1 2 | x = 'GACTGAACTGCACTTTGGTTTCATATTATTTGCTC'
extrPseKNC(x)
|
Xc1.AAA Xc1.AAC Xc1.AAG Xc1.AAT Xc1.ACA Xc1.ACC
0.000 0.014 0.000 0.000 0.000 0.000
Xc1.ACG Xc1.ACT Xc1.AGA Xc1.AGC Xc1.AGG Xc1.AGT
0.000 0.041 0.000 0.000 0.000 0.000
Xc1.ATA Xc1.ATC Xc1.ATG Xc1.ATT Xc1.CAA Xc1.CAC
0.014 0.000 0.000 0.027 0.000 0.014
Xc1.CAG Xc1.CAT Xc1.CCA Xc1.CCC Xc1.CCG Xc1.CCT
0.000 0.014 0.000 0.000 0.000 0.000
Xc1.CGA Xc1.CGC Xc1.CGG Xc1.CGT Xc1.CTA Xc1.CTC
0.000 0.000 0.000 0.000 0.000 0.014
Xc1.CTG Xc1.CTT Xc1.GAA Xc1.GAC Xc1.GAG Xc1.GAT
0.027 0.014 0.014 0.014 0.000 0.000
Xc1.GCA Xc1.GCC Xc1.GCG Xc1.GCT Xc1.GGA Xc1.GGC
0.014 0.000 0.000 0.014 0.000 0.000
Xc1.GGG Xc1.GGT Xc1.GTA Xc1.GTC Xc1.GTG Xc1.GTT
0.000 0.014 0.000 0.000 0.000 0.014
Xc1.TAA Xc1.TAC Xc1.TAG Xc1.TAT Xc1.TCA Xc1.TCC
0.000 0.000 0.000 0.027 0.014 0.000
Xc1.TCG Xc1.TCT Xc1.TGA Xc1.TGC Xc1.TGG Xc1.TGT
0.000 0.000 0.014 0.027 0.014 0.000
Xc1.TTA Xc1.TTC Xc1.TTG Xc1.TTT Xc2.lambda.1
0.014 0.014 0.027 0.041 0.550
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