Predict effector — predict_effector • deepredeff

predict_effector is used to predict effector protein given amino acid protein sequences.

predict_effector(input, taxon)

# S3 method for character
predict_effector(input, taxon)

# S3 method for data.frame
predict_effector(input, taxon)

# S3 method for AAStringSet
predict_effector(input, taxon)

# S3 method for AAString
predict_effector(input, taxon)

# S3 method for default
predict_effector(input, taxon)

Arguments

input: Input data that contains amino acid sequence(s). It can be in fasta format, strings, AAString, AAStringset, and dataframe.
taxon: Taxon group of input data. Available taxons are bacteria, fungi, and oomycete.

Value

predict_effector returns an object of class "tbl_deepredeff" or for multiple responses of class c("tbl_deepredeff", "data.frame").

An object of class "tbl_deepredeff" is a data frame containing at least the following components:

sequence: the sequence(s) from the input data.
s_score: score obtained from sigmoid function showing how likely the sequences to be an effector.
prediction: class prediction for each sequence, obtained from s_score. If the value of s_score >= 0.5, it will be classified as an effector. Otherwise, it will be classified as a non-effector.

Examples

# \donttest{
# FASTA input
input_fasta <- system.file("extdata/example/fungi_sample.fasta", package = "deepredeff")

pred_result <- deepredeff::predict_effector(
  input = input_fasta,
  taxon = "fungi"
)
#> List of 22
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