% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/idprofile.R
\name{idprofile}
\alias{idprofile}
\title{IDp PRofile From idpr Package}
\usage{
idprofile(
sequence,
uniprotAccession = NA,
proteinName = NA,
iupredType = "long",
window = 9,
pH = 7.2,
pKaSet = "IPC_protein",
structuralTendencyType = "bar",
structuralTendencySummarize = FALSE,
disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G"),
disorderNeutral = c("D", "T", "R"),
orderPromoting = c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C")
)
}
\arguments{
\item{sequence}{amino acid sequence as a single character string or vector of
single characters. It also supports a single character string that
specifies the location of a .fasta or .fa file.}
\item{uniprotAccession}{character string specifying the UniProt Accession of
the protein of interest. Used to fetch predictions from IUPreds REST API.
Default is NA. Keep as NA if you do not have a UniProt Accession.}
\item{proteinName}{character string, optional.
Used to add protein name to the title in ggplot.}
\item{iupredType}{character string specifying the type of IUPred2 prediction
to retrieve. Can be c("long", "short", "glob", "anchor", "redox"). "long"
by default. "long", "short", and "glob" use the \code{\link{iupred}}
function and specify the type of plot. Both "redox" and "anchor" use "long"
for predictions, but are context dependent. "anchor" uses
\code{\link{iupredAnchor}} to get predictions of disorder with IUPred2 and
predictions of induced folding based on ANCHOR2 predictions (Shown with a
red line). "redox" uses \code{\link{iupredRedox}} to make predictions of
disorder based on environmental conditions. Regions of predicted
environmental sensitivity are highlighted. See the respective functions
for more details. This is skipped if uniprotAccession = NA.}
\item{window}{a positive, odd integer. 51 by default.
Sets the size of sliding window, must be an odd number.
The window determines the number of residues to be analyzed and averaged
for each position along the sequence. 51 is default for
\code{\link{foldIndexR}}\cr.}
\item{pH}{numeric value, 7.0 by default.
The environmental pH used to calculate residue charge.}
\item{pKaSet}{A character string or data frame. "IPC_protein" by default.
Character string to load specific, preloaded pKa sets.
c("EMBOSS", "DTASelect", "Solomons", "Sillero", "Rodwell",
"Lehninger", "Toseland", "Thurlkill", "Nozaki", "Dawson",
"Bjellqvist", "ProMoST", "Vollhardt", "IPC_protein", "IPC_peptide")
Alternatively, the user may supply a custom pKa dataset.
The format must be a data frame where:
Column 1 must be a character vector of residues named "AA" AND
Column 2 must be a numeric vector of pKa values.}
\item{structuralTendencyType}{a character string specifying the type of plot
the \code{\link{structuralTendencyPlot}} should output.
Can be "bar" or "pie".
Equivalent argument to graphType= in the linked function.
"bar" by default.}
\item{structuralTendencySummarize}{a logical value specifying the
\code{\link{structuralTendencyPlot}} should be summarized into broad
categories. Equivalent argument to summarize= in the linked function.
FALSE by default}
\item{disorderPromoting, disorderNeutral, orderPromoting}{character vectors
of individual residues to be matched with the input sequence. Defaults:
\itemize{
\item disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G")
\item orderPromoting =
c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C")
\item disorderNeutral = c("D", "T", "R")
}
It is not recommended to change these. Arguments passed to
\code{\link{structuralTendencyPlot}}}
}
\value{
4 or 5 plots, depending if a UniProt Accession is provided.
}
\description{
The IDPRofile is a summation of many features of the idpr package,
conveniently grouped into one function for quick analysis. This combines
many plotting functions in this package. These include:\cr
\code{\link{chargeHydropathyPlot}}\cr
\code{\link{chargeCalculationLocal}}\cr
\code{\link{scaledHydropathyLocal}}\cr
\code{\link{structuralTendencyPlot}}\cr
\code{\link{foldIndexR}}\cr
All of the above linked functions only require the sequence argument
to output plots of characteristics associated with IDPs. The function also
includes options for IUPred functions. The function does one of the
following based on user-specified parameters:\cr
\code{\link{iupred}}\cr
\code{\link{iupredAnchor}}\cr
\code{\link{iupredRedox}}\cr
The IUPred function used depends on the argument of iupredType. All
require the UniProt Accession to make a proper connection to the IUPred2A
REST API. If the UniProt Accession is not specified, the IUPred plot is
skipped.
}
\section{Citations for each Plot}{
\itemize{
\item \code{\link{chargeHydropathyPlot}}
\itemize{
\item{Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator.
Biology Direct, 11(1), 55.
https://doi.org/10.1186/s13062-016-0159-9}
\item{Kyte, J., & Doolittle, R. F. (1982).
A simple method for displaying the hydropathic character
of a protein. Journal of molecular biology, 157(1), 105-132.}
\item{Uversky, V. N. (2016). Paradoxes and wonders of intrinsic
disorder: Complexity of simplicity. Intrinsically Disordered
Proteins, 4(1), e1135015.
https://doi.org/10.1080/21690707.2015.1135015}
\item{Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000).
Why are “natively unfolded” proteins unstructured under
physiologic conditions?. Proteins: structure, function,
and bioinformatics, 41(3), 415-427.
https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}
\item{If a pKa set is specified, see \code{\link{pKaData}}}
}
\item \code{\link{chargeCalculationLocal}}
\itemize{
\item{Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator.
Biology Direct, 11(1), 55.
https://doi.org/10.1186/s13062-016-0159-9}
\item{If a pKa set is specified, see \code{\link{pKaData}}}
}
\item \code{\link{scaledHydropathyLocal}}
\itemize{
\item{Kyte, J., & Doolittle, R. F. (1982).
A simple method for displaying the hydropathic character
of a protein. Journal of molecular biology, 157(1), 105-132.}
}
\item \code{\link{structuralTendencyPlot}}
\itemize{
\item{Uversky, V. N. (2013).
A decade and a half of protein intrinsic disorder:
Biology still waits for physics.
Protein Science, 22(6), 693-724.
doi:10.1002/pro.2261 }
}
\item \code{\link{foldIndexR}}
\itemize{
\item{Prilusky, J., Felder, C. E., et al. (2005).
FoldIndex: a simple tool to predict whether
a given protein sequence is intrinsically unfolded.
Bioinformatics, 21(16), 3435-3438.}
\item{Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000).
Why are “natively unfolded” proteins unstructured under
physiologic conditions?. Proteins: structure, function,
and bioinformatics, 41(3), 415-427.
https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}
\item{Also see citations for hydrapthy and charge plots above}
}
\item \code{\link{iupred}},
\code{\link{iupredAnchor}},
\code{\link{iupredRedox}}
\itemize{
\item{Bálint Mészáros, Gábor Erdős, Zsuzsanna Dosztányi, IUPred2A:
context-dependent prediction of protein disorder as a function of
redox state and protein binding, Nucleic Acids Research, Volume 46,
Issue W1, 2 July 2018, Pages W329–W337,
https://doi.org/10.1093/nar/gky384}
\item{Erdős, G., & Dosztányi, Z. (2020). Analyzing protein disorder
with IUPred2A. Current Protocols in Bioinformatics, 70, e99.
https://doi.org/10.1002/cpbi.99}
}
}
}
\examples{
#For most functions, a protein sequence is all that is needed.
#The UniProt ID is optional but recommended for IUPred results.
proteinID <- "P04637"
p53Seq <- idpr:::TP53Sequences[2]
\dontrun{
idprofile(
sequence = p53Seq,
uniprotAccession = proteinID)
#changing the iupred to redox
## and getting a pie chart for structuralTendency.
idprofile(
sequence = p53Seq,
uniprotAccession = proteinID,
pKaSet = EMBOSS,
iupredType = "redox",
structuralTendencyType = "pie")
}
}
\seealso{
\code{\link{chargeHydropathyPlot}}\cr
\code{\link{chargeCalculationLocal}}\cr
\code{\link{scaledHydropathyLocal}}\cr
\code{\link{structuralTendencyPlot}}\cr
\code{\link{foldIndexR}}\cr
\code{\link{iupred}}\cr
\code{\link{iupredAnchor}}\cr
\code{\link{iupredRedox}}
}
