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minor changes in package vignette; version number bumped to 1.4.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/msa@118901 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 23/06/2016 13:32:48
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@@ -1,8 +1,8 @@
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.4.2
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-Date: 2016-05-02
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+Version: 1.4.3
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+Date: 2016-06-23
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -1,6 +1,13 @@
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 Change history of package msa:
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 ==============================
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+Version 1.4.3:
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+- minor changes in package vignette
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+
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+Versions 1.4.1 / 1.4.2:
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+- version number bumps for technical reasons related to Bioconductor
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+  build servers
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+
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 Version 1.4.0:
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 - release as part of Bioconductor 3.3
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@@ -9,6 +9,23 @@
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   pages =	 {135--139}
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 }
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+@incollection{CharifLobry2007,
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+  author =	 {D. Charif and J. R. Lobry},
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+  title =	 {Seqin{R} 1.0-2: a contributed package to the {R}
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+                  project for statistical computing devoted to
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+                  biological sequences retrieval and analysis},
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+  booktitle =	 {Structural approaches to sequence evolution:
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+                  Molecules, networks, populations},
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+  year =	 2007,
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+  editor =	 {U. Bastolla and M. Porto and H. E. Roman and
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+                  M. Vendruscolo},
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+  series =	 {Biological and Medical Physics, Biomedical
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+                  Engineering},
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+  pages =	 {207--232},
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+  address =	 {New York},
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+  publisher =	 {Springer}
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+}
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+
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 @article{Eddelbuettel2011,
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   title =	 {{Rcpp}: Seamless {R} and {C++} Integration},
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   author =	 {D. Eddelbuettel and R. Fran\c{c}ois},
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@@ -103,6 +120,35 @@
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   pages =	 {205--217}
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 }
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+@article{ParadisClaudeStrimmer2004,
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+  title =	 {A{PE}: analyses of phylogenetics and evolution in
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+                  {R} language},
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+  author =	 {E. Paradis and J. Claude and K. Strimmer},
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+  journal =	 {Bioinformatics},
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+  year =	 2004,
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+  volume =	 20,
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+  pages =	 {289--290},
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+}
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+
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+@manual{PeleBecuAbdiChabbert2012,
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+  title =	 {{bios2mds: From BIOlogical Sequences to
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+                  MultiDimensional Scaling}},
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+  author =	 {J. Pele with J.-M. Becu and H. Abdi and
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+                  M. Chabbert},
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+  year =	 2012,
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+  note =	 {R package version 1.2.2}
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+}
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+
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+@article{Schliep2011,
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+  title =	 {phangorn: phylogenetic analysis in {R}},
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+  author =	 {K. P. Schliep},
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+  journal =	 {Bioinformatics},
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+  year =	 2011,
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+  volume =	 27,
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+  number =	 4,
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+  pages =	 {592--593},
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+}
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+
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 @article{Sievers2011,
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   author =	 {F. Sievers and A. Wilm and D. Dineen and
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                   T. J. Gibson and K. Karplus and W. Li and R. Lopez
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@@ -135,3 +181,12 @@
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   publisher =	 {Chapman \&\ Hall/CRC},
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   year =	 2014
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 }
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+
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+@article{YuSmithZhuGuanLam2016,
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+  title =	 {ggtree: an {R} package for visualization and
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+                  annotation of phylogenetic tree with different types
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+                  of meta-data},
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+  author =	 {G. Yu and D. Smith and H. Zhu and Y. Guan and
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+                  T. T. Y. Lam},
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+  year =	 {submitted}
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+}
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@@ -440,8 +440,10 @@ sequence alignments. The \msa\ package does not directly interface to any of the
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 in order to avoid dependencies and possible incompatibilities. However, \msa\ provides
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 a function \verb+msaConvert()+ that allows for converting multiple sequence alignment
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 objects to other types/classes. Currently, two such conversions are available, namely to
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-objects of class \verb+alignment+ (as defined and used by the \verb+seqinr+ package) and
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-to objects of class \verb+align+ (as defined and used by the \verb+bios2mds+ package).
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+objects of class \verb+alignment+ (as defined and used by the \verb+seqinr+ package
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+\cite{CharifLobry2007}) and
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+to objects of class \verb+align+ (as defined and used by the \verb+bios2mds+ package
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+\cite{PeleBecuAbdiChabbert2012}).
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 Note that the conversion is performed without loading or depending on the respective
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 packages.
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... ...
@@ -478,6 +480,20 @@ hemoAln3 <- msaConvert(hemoAln, type="bios2mds::align")
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 str(hemoAln3)
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 @
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+The conversions to the standard \verb+Biostrings+ classes are straightforward using
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+standard \verb+as()+ methods and not provided by the \verb+msaConvert()+ function.
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+The following example converts a multiple alignment object to class \verb+BStringSet+
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+(e.g.\ the \verb+msaplot()+ function from the \verb+ggtree+ package
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+\cite{YuSmithZhuGuanLam2016} accepts \verb+BStringSet+ objects):
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+<<Hemoglobin4>>=
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+hemoAln4 <- as(hemoAln, "BStringSet")
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+hemoAln4
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+@
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+
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+\notebox{The \texttt{msaConvert()} function has been introduced in version 1.3.3 of the
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+  \MSA\ package. So, to have this function available, at least Bioconductor 3.3
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+  is required, which requires at least R 3.3.0.}
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+
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 \section{Pretty-Printing Multiple Sequence Alignments}\label{sec:msaPrettyPrint}
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 As already mentioned above, the \MSA\ package offers the function
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@@ -817,6 +833,11 @@ bibliography below).
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 \section{Change Log}
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 \begin{description}
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+\item[Version 1.4.3:] \mbox{ }  \begin{itemize}
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+   \item minor changes in package vignette
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+  \end{itemize}
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+\item[Versions 1.4.1 and 1.4.2:] version number bumps for technical reasons
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+  related to Bioconductor build servers
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 \item[Version 1.4.0:] release as part of Bioconductor 3.3
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 \item[Version 1.3.7:] \mbox{ }  \begin{itemize}
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    \item fixes in \verb+msaPrettyPrint()+ function
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@@ -847,7 +868,7 @@ bibliography below).
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 \item[Version 1.3.1:] \mbox{ }  \begin{itemize}
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    \item fixes in Makefiles and Makevars files to account for changes in build system
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   \end{itemize}
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-\item[Version 1.3.0:] devel branch created from version 1.2.0
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+\item[Version 1.3.0:] new branch for Bioconductor 3.3 devel
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 \item[Version 1.2.0:] release as part of Bioconductor 3.2
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 \item[Version 1.1.3:] \mbox{ }  \begin{itemize}
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     \item bug fix related to custom substitution matrices
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@@ -872,84 +893,11 @@ bibliography below).
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 \item[Version 1.1.1:]  \mbox{ }  \begin{itemize}
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     \item fix of \verb+msa()+ function
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   \end{itemize}
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-\item[Version 1.1.0:] devel branch created from version 1.0.0
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+\item[Version 1.1.0:] new branch for Bioconductor 3.2 devel
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 \item[Version 1.0.0:] first official release as part of Bioconductor 3.1
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 \end{description}
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-%\bibliographystyle{plain}
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-%\bibliography{lit}
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-
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-\begin{thebibliography}{10}
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-
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-\bibitem{Beitz2000}
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-E.~Beitz.
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-\newblock {\TeX shade}: shading and labeling of multiple sequence alignments
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-  using {\LaTeX2e}.
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-\newblock {\em Bioinformatics}, 16(2):135--139, 2000.
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-
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-\bibitem{Edgar2004b}
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-R.~C. Edgar.
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-\newblock {MUSCLE}: a multiple sequence alignment method with reduced time and
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-  space complexity.
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-\newblock {\em BMC Bioinformatics}, 5(5):113, 2004.
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-
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-\bibitem{Edgar2004a}
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-R.~C. Edgar.
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-\newblock {MUSCLE:} multiple sequence alignment with high accuracy and high
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-  throughput.
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-\newblock {\em Nucleic Acids Res.}, 32(5):1792--1797, 2004.
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-
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-\bibitem{Lamport1999}
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-L.~Lamport.
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-\newblock {\em {\LaTeX} --- A Document Preparation System. User's Guide and
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-  Reference Manual}.
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-\newblock Addison-Wesley Longman, Amsterdam, 1999.
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-
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-\bibitem{Leisch2002}
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-F.~Leisch.
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-\newblock Sweave: dynamic generation of statistical reports using literate data
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-  analysis.
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-\newblock In W.~H\"ardle and B.~R\"onz, editors, {\em Compstat 2002 ---
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-  Proceedings in Computational Statistics}, pages 575--580, Heidelberg, 2002.
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-  Physica-Verlag.
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-
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-\bibitem{Morgenstern1999}
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-B.~Morgenstern.
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-\newblock {DIALIGN 2}: improvement of the segment-to-segment approach to
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-  multiple sequence alignment.
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-\newblock {\em Bioinformatics}, 15(3):211--218, 1999.
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-
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-\bibitem{Nethercote2007}
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-N.~Nethercote and J.~Seward.
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-\newblock Valgrind: A framework for heavyweight dynamic binary instrumentation.
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-\newblock In {\em Proc. of the ACM SIGPLAN 2007 Conf. on Programming Language
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-  Design and Implementation}, San Diego, CA, 2007.
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-
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-\bibitem{Notredame2000}
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-C.~Notredame, D.~G. Higgins, and J.~Heringa.
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-\newblock {T-Coffee}: A novel method for fast and accurate multiple sequence
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-  alignment.
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-\newblock {\em J. Mol. Biol.}, 302(1):205--217, 2000.
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-
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-\bibitem{Sievers2011}
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-F.~Sievers, A.~Wilm, D.~Dineen, T.~J. Gibson, K.~Karplus, W.~Li, R.~Lopez,
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-  H.~McWilliam, M.~Remmert, J.~S\"oding, J.~D. Thompson, and D.~G. Higgins.
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-\newblock Fast, scalable generation of high-quality protein multiple sequence
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-  alignments using {Clustal Omega}.
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-\newblock {\em Mol. Syst. Biol.}, 7:539, 2011.
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-
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-\bibitem{Thompson1994}
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-J.~D. Thompson, D.~G. Higgins, and T.~J. Gibson.
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-\newblock {CLUSTAL W}: improving the sensitivity of progressive multiple
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-  sequence alignment through sequence weighting, position-specific gap
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-  penalties and weight matrix choice.
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-\newblock {\em Nucleic Acids Res.}, 22(22):4673--4680, 2004.
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-
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-\bibitem{Xie2014}
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-Y.~Xie.
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-\newblock {\em Dynamic Documents with R and knitr}.
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-\newblock Chapman \&\ Hall/CRC, 2014.
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-
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-\end{thebibliography}
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+\bibliographystyle{plain}
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+\bibliography{lit}
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 \end{document}