Description Usage Arguments Value Examples
This function predicts the probability of a protein to be an antimicrobial peptide
1 | predict_amps(faa_df, min_len = 5, n_cores = 1, model = "precursor")
|
faa_df |
A dataframe obtained from |
min_len |
The minimum protein length for which predictions will be generated |
n_cores |
On multicore machines split the task across this many processors. This option does not work on Windows |
model |
Either a string with the name of a built-in model (mature, precursor), OR, A train object suitable for passing to the predict.train function in the caret package. If omitted the default model will be used. |
The original input data.frame with a new column added called prob_AMP
with the probability of that sequence to be an antimicrobial peptide. Any sequences that are too short or which contain invalid amin acids will have NA in this column
1 2 3 4 5 | my_bat_faa_df <- read_faa(system.file("extdata/bat_protein.fasta", package = "ampir"))
predict_amps(my_bat_faa_df)
# seq_name prob_AMP
# [1] G1P6H5_MYOLU 0.9723796
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