predict_effector {deepredeff}

Predict effector

Description

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

Usage

predict_effector(input, taxon)

## S3 method for class 'character'
predict_effector(input, taxon)

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

## S3 method for class 'AAStringSet'
predict_effector(input, taxon)

## S3 method for class 'AAString'
predict_effector(input, taxon)

## Default S3 method:
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

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

pred_result <- deepredeff::predict_effector(
  input = input_fasta,
  taxon = "fungi"
)