Recognizes antimicrobial peptides using the AmpGram algorithm.
# S3 method for ampgram_model
predict(object, newdata, ...)ampgram_model object.
list of sequences (for example as given by
read_fasta or read_txt).
further arguments passed to or from other methods.
list of objects of class single_ampgram_pred. Each object
of this class contains analyzed sequence, values of predictions for 10-mers and
result of the prediction for the whole peptide/protein.
AmpGram requires the external package, AmpGramModel, which
contains models necessary to perform the prediction. The model
can be installed using install_AmpGramModel.
Predictions for each protein are stored in objects of class
single_ampgram_pred. It consists of three elements:
Character vector of amino acid sequence of an analyzed peptide/protein
Numeric vector of predictions for each 10-mer (subsequence of 10 amino acids) of a sequence. Prediction value indicates probability that a 10-mer possesses antimicrobial activity and ranges from 0 (non-AMP) to 1 (AMP).
Named numeric vector of a single prediction value for
a whole peptide/protein. Its value corresponds to the probability that a
peptide/protein exhibits antimicrobial activity. It assumes name TRUE
if probability is equal or greater than 0.5, i.e. peptide/protein is classified
as antimicrobial (AMP), and FALSE if probability is less that 0.5,
i.e. peptide/protein is classified as non-antimicrobial (non-AMP).