get_netGPI: Query NetGPI - 1.1 web server.

In missuse/ragp: Mining for Hydroxyproline rich glycoprotein sequences

Description

NetGPI server offers GPI Anchor predictions

Usage

get_netGPI(data, ...)

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

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

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

## Default S3 method:
get_netGPI(data = NULL, sequence, id, ...)

## S3 method for class '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.

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.

Source

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

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

See Also

get_big_pi get_pred_gpi

Examples

library(ragp)
netGPI_pred <- get_netGPI(data = at_nsp[1:10,],
                          sequence,
                          Transcript.id)
netGPI_pred

missuse/ragp documentation built on Jan. 4, 2022, 10:49 a.m.