Query NetGPI - 1.1 web server. — get

NetGPI server offers GPI Anchor predictions

get_netGPI(data, ...)

# S3 method for character
get_netGPI(data, splitter = 2500L, attempts = 2, progress = FALSE, ...)

# S3 method for data.frame
get_netGPI(data, sequence, id, ...)

# S3 method for list
get_netGPI(data, ...)

# S3 method for default
get_netGPI(data = NULL, sequence, id, ...)

# S3 method for AAStringSet
get_netGPI(data, ...)

Arguments

data	A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class `SeqFastaAA` resulting from `read.fasta` call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
...	currently no additional arguments are accepted apart the ones documented bellow.
splitter	An integer indicating the number of sequences to be in each .fasta file that is to be sent to the server. Defaults to 2500. Change only in case of a server side error. Accepted values are in range of 1 to 5000.
attempts	Integer, number of attempts if server unresponsive, at default set to 2.
progress	Boolean, whether to show the progress bar, at default set to FALSE.
sequence	A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.
id	A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank.

Source

https://services.healthtech.dtu.dk/service.php?NetGPI-1.1

Value

A data frame with columns:

id: Character, as from input
length: Integer, length of the protein sequence
is.gpi: Logical, is the protein predicted to be GPI anchored.
omega_site: Integer, indicating the sequence position of the omega-site.
likelihood: Numeric, likelihood of the prediction.

Note

This function creates temporary files in the working directory.

References

Gislason MH. Nielsen H. Armenteros JA. AR Johansen AR. (2019) Prediction of GPI-Anchored proteins with pointer neural networks. bioRxiv. doi: https://doi.org/10.1101/838680

Examples


library(ragp)
netGPI_pred <- get_netGPI(data = at_nsp[1:10,],
                          sequence,
                          Transcript.id)
netGPI_pred
#>             id length is.gpi omega_site likelihood
#> 1  ATCG00660.1    117  FALSE         NA      0.996
#> 2  AT2G43600.1    273  FALSE         NA      0.992
#> 3  AT2G28410.1    115   TRUE         95      0.321
#> 4  AT2G22960.1    184  FALSE         NA      0.993
#> 5  AT2G19580.1    270  FALSE         NA      0.988
#> 6  AT2G19690.2    148  FALSE         NA      0.992
#> 7  AT2G19690.1    147  FALSE         NA      0.994
#> 8  AT2G33130.1    103  FALSE         NA      0.987
#> 9  AT2G05520.1    145  FALSE         NA      0.993
#> 10 AT2G05520.2    138  FALSE         NA      0.993