PredCRG_Enc: Encoding of protein sequence data in to numeric feature...
In PredCRG: Computational Prediction of Proteins Encoded by Circadian Genes
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Before using the protein sequences for prediction using the proposed model, the sequences must be transformed into numeric feature vectors. The function PredCRG_Enc will transform each protein sequnces to a numeric vector of 62 observations, based on the compositional, physico-chemical and transitional features used in the PredCRG model.
Usage
1
PredCRG_Enc(prot_seq)
Arguments
prot_seq
Sequence dataset to be supplied as input, must be an object of class AAStringSet
Details
The dataset must contains the protein sequences having standard amino acid residues only. The clas AAStringSet can be obtained by reading the FASTA file using readAAStringSet available in bioconductor package Biostrings.
Value
A matrix of dimension n*62, for n number of sequences.
Author(s)
Prabina Kumar Meher, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, INDIA
See Also
PredCRG, PredCRG_training, model1, model2,model3,model4
Examples
1
2
3
4
data(test)
enc <- PredCRG_Enc(test)#encoding of test sequence data
enc[1:5,1:5]
PredCRG documentation built on Dec. 15, 2020, 5:35 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Before using the protein sequences for prediction using the proposed model, the sequences must be transformed into numeric feature vectors. The function PredCRG_Enc will transform each protein sequnces to a numeric vector of 62 observations, based on the compositional, physico-chemical and transitional features used in the PredCRG model.
Usage
1 | PredCRG_Enc(prot_seq)
|
Arguments
prot_seq |
Sequence dataset to be supplied as input, must be an object of class |
Details
The dataset must contains the protein sequences having standard amino acid residues only. The clas AAStringSet can be obtained by reading the FASTA file using readAAStringSet available in bioconductor package Biostrings.
Value
A matrix of dimension n*62, for n number of sequences.
Author(s)
Prabina Kumar Meher, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, INDIA
See Also
PredCRG, PredCRG_training, model1, model2,model3,model4
Examples
1 2 3 4 | data(test)
enc <- PredCRG_Enc(test)#encoding of test sequence data
enc[1:5,1:5]
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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