Add links to documentation

R/get_big_pi.R

@@ -3,7 +3,7 @@
 #' big-PI Plant Predictor is a web server utilizing a scoring algorithm for prediction of GPI modification sites in plants.
 #'
 #' @aliases get_big_pi get_big_pi.default get_big_pi.character get_big_pi.data.frame get_big_pi.list get_big_pi.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param simplify A boolean indicating the type of returned object, defaults to TRUE.

R/get_espritz.R

@@ -3,7 +3,7 @@
 #' Espritz web server predicts disordered regions from primary sequence. It utilizes Bi-directional Recursive Neural Networks and can process proteins on a genomic scale with little effort and state-of-the-art accuracy.
 #'
 #' @aliases get_espritz get_espritz.default get_espritz.character get_espritz.data.frame get_espritz.list get_espritz.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param model One of c('X-Ray', 'Disprot', 'NMR'), default is 'X-Ray'. Determines the model to be used for prediction. See details.

R/get_hmm.R

@@ -4,7 +4,7 @@
 #' of a protein sequence vs a profile-HMM database (Pfam-A).
 #'
 #' @aliases get_hmm get_hmm.default get_hmm.character get_hmm.data.frame get_hmm.list get_hmm.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param verbose Boolean, whether to print out the output for each sequence, defaults to FALSE.

R/get_netGPI.R

@@ -3,7 +3,7 @@
 #' NetGPI server offers GPI Anchor predictions
 #'
 #' @aliases get_netGPI get_netGPI.default get_netGPI.character get_netGPI.data.frame get_netGPI.list get_netGPI.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param 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.

R/get_phobius.R

@@ -3,7 +3,7 @@
 #' Phobius web server is a combined transmembrane topology and signal peptide (N-sp) predictor. Currently only "normal prediction" of signal peptides is supported by the function.
 #'
 #' @aliases get_phobius get_phobius.default get_phobius.character get_phobius.data.frame get_phobius.list get_phobius.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param progress Boolean, whether to show the progress bar, at default set to FALSE.

R/get_pred_gpi.R

@@ -3,7 +3,7 @@
 #' PredGPI web server is a predictor of GPI modification sites.
 #'
 #' @aliases get_pred_gpi get_pred_gpi.default get_pred_gpi.character get_pred_gpi.data.frame get_pred_gpi.list get_pred_gpi.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param spec Numeric in the 0-1 range, indicating the threshold specificity.

R/get_signalp.R

@@ -3,7 +3,7 @@
 #' SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
 #'
 #' @aliases get_signalp get_signalp.default get_signalp.character get_signalp.data.frame get_signalp.list get_signalp.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param org_type One of c("euk", "gram-", "gram+"), defaults to "euk". Which model should be used for prediction.

R/get_signalp5.R

@@ -3,7 +3,7 @@
 #' The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya.
 #'
 #' @aliases get_signalp5 get_signalp5.default get_signalp5.character get_signalp5.data.frame get_signalp5.list get_signalp5.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param org_type One of "euk", "gram-", "gram+" or "archea". Default is "euk". Are the protein sequences from Eukarya, Gram-negative Bacteria, Gram-positive Bacteria or Archaea.

R/get_targetp.R

@@ -3,7 +3,7 @@
 #' TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). TargetP uses ChloroP and SignalP to predict cleavage sites for cTP and SP, respectively. For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.
 #'
 #' @aliases get_targetp get_targetp.default get_targetp.character get_targetp.data.frame get_targetp.list get_targetp.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param org_type One of c("non_plant", "plant"), defaults to "plant". Which models should be used for prediction.

R/get_tmhmm.R

@@ -3,7 +3,7 @@
 #' TMHMM server offers prediction of transmembrane helices in proteins
 #'
 #' @aliases get_tmhmm get_tmhmm.default get_tmhmm.character get_tmhmm.data.frame get_tmhmm.list
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param splitter An integer indicating the number of sequences to be in each .fasta file that is to be sent to the server. Default is 2500. Change only in case of a server side error. Accepted values are in range of 1 to 10000.

R/maab.R

@@ -3,7 +3,7 @@
 #' Perform Motif and amino acid bias classification of hydroxyproline rich glycoproteins according to Johnson et al. (2017)
 #' 
 #' @aliases maab maab.default maab.character maab.data.frame maab.list maab.AAStringSet
-#' @param 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 \code{\link[seqinr]{read.fasta}} call. Alternatively an `AAStringSet` object. Should be left blank if vectors are provided to sequence and id arguments.
+#' @param 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 \code{\link[seqinr]{SeqFastaAA}} resulting from \code{\link[seqinr]{read.fasta}} call. Alternatively an \code{\link[Biostrings]{AAStringSet}} object. Should be left blank if vectors are provided to sequence and id arguments.
 #' @param 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.
 #' @param 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.
 #' @param order Order of motif counting, the default is as in Johnson et al. (2017).