Description Usage Arguments Value Examples
predict_effector
is used to predict effector protein given amino acid protein sequences.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
|
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. |
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:
|
the sequence(s) from the input data. |
|
score obtained from sigmoid function showing how likely the sequences to be an effector. |
|
class prediction for each sequence, obtained from s_score. If the value of |
1 2 3 4 5 6 7 | # FASTA input
input_fasta <- system.file("extdata/example/fungi_sample.fasta", package = "deepredeff")
pred_result <- deepredeff::predict_effector(
input = input_fasta,
taxon = "fungi"
)
|
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