diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0bfedb6..c30b41e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -20,8 +20,6 @@ jobs: fail-fast: false matrix: config: - - {os: ubuntu-latest, r: '4.1'} - - {os: ubuntu-latest, r: '4.2'} - {os: ubuntu-latest, r: '4.3'} - {os: ubuntu-latest, r: '4.4'} - {os: ubuntu-latest, r: 'release'} @@ -48,11 +46,32 @@ jobs: needs: check - uses: r-lib/actions/setup-tinytex@v2 - - name: Install TinyTeX fonts needed for vignette PDF rendering - run: tinytex::tlmgr_install("bera") + - name: Install LaTeX packages needed for BiocStyle vignette + run: | + tinytex::tlmgr_install(c( + "bera", + "nowidow", + "parnotes", + "titlesec", + "enumitem", + "parskip", + "fancyhdr", + "footmisc", + "placeins", + "ragged2e", + "changepage", + "xstring", + "caption", + "preprint", + "soul", + "marginfix", + "mathtools", + "framed" + )) shell: Rscript {0} - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' + error-on: '"error"' diff --git a/.gitignore b/.gitignore index 807ea25..806598d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,14 @@ .Rproj.user .Rhistory .RData + +# LaTeX / vignette build artifacts +*.aux +*.bbl +*.blg +*.log +*.out +*.toc +*-concordance.tex +vignettes/*.tex +vignettes/*.pdf diff --git a/R/pISVM.R b/R/pISVM.R index 76f5333..68090e0 100644 --- a/R/pISVM.R +++ b/R/pISVM.R @@ -355,13 +355,12 @@ aaIndex <- function(sequence){ oldw <- getOption("warn") options(warn = -1) - temp <- aaTable*aaZimmermanDes + temp <- as.vector(aaTable) * aaZimmermanDes$value options(warn = oldw) - zimm <- pKNTerm + pKCTerm + sum(temp$value) + zimm <- pKNTerm + pKCTerm + sum(temp) zimm = zimm/(length(prot)+2) return (as.numeric(zimm)) } - diff --git a/vignettes/pIR-concordance.tex b/vignettes/pIR-concordance.tex deleted file mode 100644 index 65206b7..0000000 --- a/vignettes/pIR-concordance.tex +++ /dev/null @@ -1,2 +0,0 @@ -\Sconcordance{concordance:pIR.tex:/Users/yperez/IdeaProjects/github-repo/R-packages/pIR/vignettes/pIR.Rnw:% -1 5 1 1 2 1 0 1 2 8 1 1 0 219 1 1 2 20 0 1 2 3 1} diff --git a/vignettes/pIR.aux b/vignettes/pIR.aux deleted file mode 100644 index 0f633fd..0000000 --- a/vignettes/pIR.aux +++ /dev/null @@ -1,39 +0,0 @@ -\relax -\providecommand\hyper@newdestlabel[2]{} -\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} -\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined -\global\let\oldcontentsline\contentsline -\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} -\global\let\oldnewlabel\newlabel -\gdef\newlabel#1#2{\newlabelxx{#1}#2} -\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} -\AtEndDocument{\ifx\hyper@anchor\@undefined -\let\contentsline\oldcontentsline -\let\newlabel\oldnewlabel -\fi} -\fi} -\global\let\hyper@last\relax -\gdef\HyperFirstAtBeginDocument#1{#1} -\providecommand\HyField@AuxAddToFields[1]{} -\providecommand\HyField@AuxAddToCoFields[2]{} -\bibstyle{/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BiocStyle/resources/tex/unsrturl} -\citation{perez2012} -\citation{bjellqvist1993} -\@writefile{toc}{\contentsline {section}{\numberline {1}Compute isoelectric protein of peptides and proteins}{1}{section.1}} -\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Iterative Method}{1}{subsection.1.1}} -\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces pK values for the Iterative method}}{2}{table.1}} -\newlabel{my-label}{{1}{2}{pK values for the Iterative method}{table.1}{}} -\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.1.1}Calculate isoelectric point}{2}{subsubsection.1.1.1}} -\citation{bjellqvist1993} -\citation{bjellqvist1993} -\citation{gauci2008} -\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.1.2}Compute pI using all the pk sets}{3}{subsubsection.1.1.2}} -\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Bjellqvist Method}{4}{subsection.1.2}} -\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.1}Calculate isoelectric point}{4}{subsubsection.1.2.1}} -\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.2}Compute pI using all the pk sets}{4}{subsubsection.1.2.2}} -\bibdata{Bioc} -\bibcite{perez2012}{1} -\bibcite{bjellqvist1993}{2} -\bibcite{gauci2008}{3} -\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}SVM Method}{5}{subsection.1.3}} -\@writefile{toc}{\contentsline {section}{\numberline {2}Session info}{5}{section.2}} diff --git a/vignettes/pIR.bbl b/vignettes/pIR.bbl deleted file mode 100644 index e54d043..0000000 --- a/vignettes/pIR.bbl +++ /dev/null @@ -1,25 +0,0 @@ -\begin{thebibliography}{1} - -\bibitem{perez2012} -Yasset Perez-Riverol, Enrique Audain, Aleli Millan, Yassel Ramos, Aniel - Sanchez, Juan~Antonio Vizca{\'\i}no, Rui Wang, Markus M{\"u}ller, Yoan~J - Machado, Lazaro~H Betancourt, et~al. -\newblock Isoelectric point optimization using peptide descriptors and support - vector machines. -\newblock {\em Journal of proteomics}, 75(7):2269--2274, 2012. - -\bibitem{bjellqvist1993} -Bengt Bjellqvist, Graham~J Hughes, Christian Pasquali, Nicole Paquet, Florence - Ravier, Jean-Charles Sanchez, S{\'e}verine Frutiger, and Denis Hochstrasser. -\newblock The focusing positions of polypeptides in immobilized ph gradients - can be predicted from their amino acid sequences. -\newblock {\em Electrophoresis}, 14(1):1023--1031, 1993. - -\bibitem{gauci2008} -Sharon Gauci, Bas Van~Breukelen, Simone~M Lemeer, Jeroen Krijgsveld, and - Albert~JR Heck. -\newblock A versatile peptide pi calculator for phosphorylated and n-terminal - acetylated peptides experimentally tested using peptide isoelectric focusing. -\newblock {\em Proteomics}, 8(23-24):4898--4906, 2008. - 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-\documentclass{article} - -\RequirePackage{/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BiocStyle/resources/tex/Bioconductor} - -\AtBeginDocument{\bibliographystyle{/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BiocStyle/resources/tex/unsrturl}} -\newcommand{\exitem}[3]{% - \item \texttt{\textbackslash#1\{#2\}} #3 \csname#1\endcsname{#2}.% -} - -\title{pIR: An \R{} package for isoelectric point prediction based on amino acid sequences} -\author{Yasset Perez-Riverol and Enrique Audain} - -\usepackage{Sweave} -\begin{document} -\input{pIR-concordance} - -\maketitle - - -%% Abstract and keywords %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\vskip 0.3in minus 0.1in -\hrule -\begin{abstract} - Accurate estimation of the isoelectric point value (pI) based on the amino acid sequence becomes critical to perform proteomics experiments. Also, it is one of the most useful electrostatic properties to study peptides and proteins. Different methods has been proposed to compute the theoretical isoelectric point of peptides and proteins using several pK sets \cite{perez2012, bjellqvist1993}. This vignette provides a brief overview of the available interface and functionality as well as a short use case. -\end{abstract} - -\textit{Keywords}: proteomics, peptides, proteins, electrophoresis, mass spectrometry, isoelectric point, tutorial. -\vskip 0.1in minus 0.05in -\hrule -\vskip 0.2in minus 0.1in -\vspace{10mm} -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - - -\tableofcontents - -\section{Compute isoelectric protein of peptides and proteins} -\subsection{Iterative Method} - Isoelectric point can be defined as the point in a titration curve at which the net surface charge of a protein or peptide equals to zero. The called \textbf{"Iterative Method"} to predict the iseoelct point only considers the contribution of individual pKa values to the Henderson-Hasselbach equation. Keeping in main this we can use Henderson-Hasselbach equation to calculate protein charge in certain pH: - -- \textbf{for negative charged macromolecules}: - -\begin{center} - \( pH = -1/(1+10^{(pK_n - pH)}) \) Equation(1) -\end{center} - -where \(pK_n\) is the acid dissociation constant of negatively charged amino acid - -- \textbf{for positive charged macromolecules}: - -\begin{center} - \( pH = 1/(1+10^{(pH - pK_p)}) \) Equation(2) -\end{center} - -where \(pK_p\) is the acid dissociation constant of positively charged amino acid - - -The most import moment during isoelectric point determination is usage of appropriate pK values. Unfortunately, there is no agreement in this matter. Each source gives different pKs. Some of them are presented pK that are available for the Iterative method in \textbf{pIR} are: - -\begin{table}[h] -\centering -\caption{pK values for the Iterative method} -\label{my-label} -\begin{tabular}{|l|l|l|l|l|l|l|l|l|l|} -\hline - & \multicolumn{9}{c|}{{\bf Amino acid}} \\ \hline -{pK value set} & NH2 & COOH & C & D & E & H & K & R & Y \\ \hline -emboss & 8.6 & 3.6 & 8.5 & 3.9 & 4.1 & 6.5 & 10.8 & 12.5 & 10.1 \\ \hline -DTASelect & 8.0 & 3.1 & 8.5 & 4.4 & 4.4 & 6.5 & 10.0 & 12.0 & 10.0 \\ \hline -solomon & 9.6 & 2.4 & 8.3 & 3.9 & 4.3 & 6.0 & 10.5 & 12.5 & 10.1 \\ \hline -sillero & 8.2 & 3.2 & 9.0 & 4.0 & 4.5 & 6.4 & 10.4 & 12.0 & 10.0 \\ \hline -rodwell & 8.0 & 3.1 & 8.33 & 3.68 & 4.25 & 6.0 & 11.5 & 11.5 & 10.07 \\ \hline -patrickios & 11.2 & 4.2 & - & 4.2 & 4.2 & - & 11.2 & 11.2 & - \\ \hline -lehninger & 9.69 & 2.34 & 8.33 & 3.86 & 4.25 & 6.0 & 10.5 & 12.4 & 10.0\\ \hline -grimsley & 7.7 & 3.3 & 6.8 & 3.5 & 4.2 & 6.6 & 10.5 & 12.04 & 10.3 \\ \hline -\end{tabular} -\end{table} - -\subsubsection{Calculate isoelectric point} - -\begin{verbatim} - - # compute the isoelectric point using solomon method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "solomon") - pI.value - # 10.526 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using rodwell method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "rodwell") - pI.value - # 11.404 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using emboss method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "emboss") - pI.value - # 10.801 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using lehninger method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "lehninger") - pI.value - # 10.530 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using grimsley method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "grimsley") - pI.value - # 10.495 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using patrickios method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "patrickios") - pI.value - # 11.200 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using DtaSelect method - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pI.value <- pIIterative(sequence = seq, pkSetMethod = "DtaSelect") - pI.value - # 10.025 - -\end{verbatim} - -\subsubsection{Compute pI using all the pk sets} - -\begin{verbatim} - # compute the isoelectric point using all pK sets - library(pIR) - seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC" - pIValue <- computeAllIterativeValues(seq = seq) - pIValue - # method values - # 1 solomon 10.526 - # 2 rodwell 11.404 - # 3 emboss 10.801 - # 4 lehninger 10.530 - # 5 grimsley 10.495 - # 6 patrickios 11.200 - # 7 DtaSelect 10.025 - -\end{verbatim} - -\subsection{Bjellqvist Method} - -The Bjellquivst method \cite{bjellqvist1993} is based on the determination of the pK differences between closely related amino acids, and it was the first algorithm that proposed a different pKa value depending on the amino acid position in the sequence. The current version of the pIR supports four different pKsets: \textbf{bjell} \cite{bjellqvist1993}, \textbf{calibrated} \cite{gauci2008}, \textbf{skoog} and \textbf{expasy} \url{http://expasy.org/} - -\subsubsection{Calculate isoelectric point} - -\begin{verbatim} - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using bjell pk set - library(pIR) - seq <- "AGAAPYVQAFDSLLAGPVAE" - pI.value <- pIBell(sequence = seq, pkSetMethod = "bjell") - pI.value - # 3.04 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using calibrated pk set - library(pIR) - seq <- "AGAAPYVQAFDSLLAGPVAE" - pI.value <- pIBell(sequence = seq, pkSetMethod = "calibrated") - pI.value - # 4.09 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using skoog pk Set - library(pIR) - seq <- "AGAAPYVQAFDSLLAGPVAE" - pI.value <- pIBell(sequence = seq, pkSetMethod = "skoog") - pI.value - # 2.93 - - # -------------------------------------------------------------------- # - - # compute the isoelectric point using expasy pK set - library(pIR) - seq <- "AGAAPYVQAFDSLLAGPVAE" - pI.value <- pIBell(sequence = seq, pkSetMethod = "expasy") - pI.value - # 4.09 - -\end{verbatim} - -\subsubsection{Compute pI using all the pk sets} - -\begin{verbatim} - # compute the isoelectric point using all the pK sets - seq <- "AGAAPYVQAFDSLLAGPVAE" - pIValue <- computeAllBjellValues(seq = seq) - pIValue - # method values - #1 expasy 4.09 - #2 skoog 2.93 - #3 calibrated 4.09 - #4 bjell 3.04 -\end{verbatim} - -\subsection{SVM Method} - - -%--------------------------------------------------------- -\section{Session info} -%--------------------------------------------------------- - -Here is the output of \Rfunction{sessionInfo} on the system on which -this document was compiled: -\begin{Schunk} -\begin{Sinput} -> toLatex(sessionInfo()) -\end{Sinput} -\begin{itemize}\raggedright - \item R version 3.2.3 (2015-12-10), \verb|x86_64-apple-darwin13.4.0| - \item Locale: \verb|C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8| - \item Base packages: base, datasets, grDevices, graphics, methods, stats, - utils - \item Other packages: pIR~0.99.0 - \item Loaded via a namespace (and not attached): BiocStyle~1.8.0, MASS~7.3-45, - Matrix~1.2-3, MatrixModels~0.4-1, Rcpp~0.12.3, SparseM~1.7, car~2.1-1, - caret~6.0-64, codetools~0.2-14, colorspace~1.2-6, corrplot~0.73, - devtools~1.10.0, digest~0.6.9, foreach~1.4.3, ggplot2~2.0.0, grid~3.2.3, - gtable~0.1.2, iterators~1.0.8, kernlab~0.9-23, knitr~1.12.3, - lattice~0.20-33, lme4~1.1-11, lsr~0.5, magrittr~1.5, memoise~1.0.0, - mgcv~1.8-11, minqa~1.2.4, munsell~0.4.3, nlme~3.1-124, nloptr~1.0.4, - nnet~7.3-12, parallel~3.2.3, pbkrtest~0.4-6, plyr~1.8.3, quantreg~5.21, - reshape2~1.4.1, roxygen2~5.0.1, scales~0.3.0, splines~3.2.3, stats4~3.2.3, - stringi~1.0-1, stringr~1.0.0, tools~3.2.3, withr~1.0.1 -\end{itemize}\end{Schunk} - -\bibliography{Bioc} - -\end{document} diff --git a/vignettes/pIR.toc b/vignettes/pIR.toc deleted file mode 100644 index cc69561..0000000 --- a/vignettes/pIR.toc +++ /dev/null @@ -1,9 +0,0 @@ -\contentsline {section}{\numberline {1}Compute isoelectric protein of peptides and proteins}{1}{section.1} -\contentsline {subsection}{\numberline {1.1}Iterative Method}{1}{subsection.1.1} -\contentsline {subsubsection}{\numberline {1.1.1}Calculate isoelectric point}{2}{subsubsection.1.1.1} -\contentsline {subsubsection}{\numberline {1.1.2}Compute pI using all the pk sets}{3}{subsubsection.1.1.2} -\contentsline {subsection}{\numberline {1.2}Bjellqvist Method}{4}{subsection.1.2} -\contentsline {subsubsection}{\numberline {1.2.1}Calculate isoelectric point}{4}{subsubsection.1.2.1} -\contentsline {subsubsection}{\numberline {1.2.2}Compute pI using all the pk sets}{4}{subsubsection.1.2.2} -\contentsline {subsection}{\numberline {1.3}SVM Method}{5}{subsection.1.3} -\contentsline {section}{\numberline {2}Session info}{5}{section.2}