get_big_pi: Query big-PI Plant Predictor web server.

In missuse/ragp: Mining for Hydroxyproline rich glycoprotein sequences

Description

big-PI Plant Predictor is a web server utilizing a scoring algorithm for prediction of GPI modification sites in plants.

Usage

get_big_pi(data, ...)

## S3 method for class 'character'
get_big_pi(data, ...)

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

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

## Default S3 method:
get_big_pi(
  data = NULL,
  sequence,
  id,
  simplify = TRUE,
  sleep = 1,
  progress = FALSE,
  ...
)

## S3 method for class 'AAStringSet'
get_big_pi(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.
sequence	An 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	An 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.
simplify	A boolean indicating the type of returned object, defaults to TRUE.
sleep	A numeric indicating the pause in seconds between server calls, at default set to 1.
progress	Boolean, whether to show the progress bar, at default set to FALSE.

Value

If simplify == TRUE:

A data frame with columns:

id

Character, indicating the protein identifier

is.gpi

Logical, did big-Pi predict the presence of a GPI

Quality

Character, indicating the quality of the highest scoring omega-site

omega_site

Integer, indicating the sequence position of the highest scoring omega-site

PValue

Numeric, indicating the p-value for the prediction of the highest scoring omega-site

If simplify == FALSE:

A list of predictions, each element named according to the sequence id, containing a two element list:

prediction

data frame, resembling the one returned by simplify == TRUE, along with alternative site predictions (if present)

calculation

data frame, with profile dependent and profile independent scores

Note

If the server is unable to make a prediction due to non-amino acid letters or length of the sequence, the returned prediction is NA (is.bigpi column).

Source

http://mendel.imp.ac.at/gpi/plant_server.html

References

Eisenhaber B. Wildpaner M. Schultz CJ. Borner GHH. Dupree P. Eisenhaber F. (2003) Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiology 133(4): 1691-701

Examples

library(ragp)
data(at_nsp)

#indexes of some sequences in at_nsp
ind <- c(129, 145, 147, 160, 170)

big_pi_pred <- get_big_pi(sequence = at_nsp$sequence[ind],
                          id = at_nsp$Transcript.id[ind],
                          simplify = FALSE)

big_pi_pred <- get_big_pi(data = at_nsp[ind,],
                          sequence = sequence,
                          id = Transcript.id,
                          simplify = TRUE)
big_pi_pred

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