[Seqinr-commits] r1689 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 5 14:20:48 CET 2009
Author: lobry
Date: 2009-11-05 14:20:48 +0100 (Thu, 05 Nov 2009)
New Revision: 1689
Modified:
pkg/inst/doc/src/mainmatter/dealseq.tex
Log:
compil R 2.10
Modified: pkg/inst/doc/src/mainmatter/dealseq.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/dealseq.tex 2009-11-05 13:20:35 UTC (rev 1688)
+++ pkg/inst/doc/src/mainmatter/dealseq.tex 2009-11-05 13:20:48 UTC (rev 1689)
@@ -139,56 +139,56 @@
methods(getFrag)
\end{Sinput}
\begin{Soutput}
-[1] getFrag.SeqAcnucWeb getFrag.SeqFastaAA getFrag.SeqFastadna
-[4] getFrag.SeqFrag getFrag.character getFrag.default
-[7] getFrag.list getFrag.logical getFrag.qaw
+[1] getFrag.character getFrag.default getFrag.list
+[4] getFrag.logical getFrag.qaw getFrag.SeqAcnucWeb
+[7] getFrag.SeqFastaAA getFrag.SeqFastadna getFrag.SeqFrag
\end{Soutput}
\begin{Sinput}
methods(getSequence)
\end{Sinput}
\begin{Soutput}
-[1] getSequence.SeqAcnucWeb getSequence.SeqFastaAA getSequence.SeqFastadna
-[4] getSequence.SeqFrag getSequence.character getSequence.default
-[7] getSequence.list getSequence.logical getSequence.qaw
+[1] getSequence.character getSequence.default getSequence.list
+[4] getSequence.logical getSequence.qaw getSequence.SeqAcnucWeb
+[7] getSequence.SeqFastaAA getSequence.SeqFastadna getSequence.SeqFrag
\end{Soutput}
\begin{Sinput}
methods(getName)
\end{Sinput}
\begin{Soutput}
-[1] getName.SeqAcnucWeb getName.SeqFastaAA getName.SeqFastadna
-[4] getName.SeqFrag getName.default getName.list
-[7] getName.logical getName.qaw
+[1] getName.default getName.list getName.logical
+[4] getName.qaw getName.SeqAcnucWeb getName.SeqFastaAA
+[7] getName.SeqFastadna getName.SeqFrag
\end{Soutput}
\begin{Sinput}
methods(getLength)
\end{Sinput}
\begin{Soutput}
-[1] getLength.SeqAcnucWeb getLength.SeqFastaAA getLength.SeqFastadna
-[4] getLength.SeqFrag getLength.character getLength.default
-[7] getLength.list getLength.logical getLength.qaw
+[1] getLength.character getLength.default getLength.list
+[4] getLength.logical getLength.qaw getLength.SeqAcnucWeb
+[7] getLength.SeqFastaAA getLength.SeqFastadna getLength.SeqFrag
\end{Soutput}
\begin{Sinput}
methods(getTrans)
\end{Sinput}
\begin{Soutput}
-[1] getTrans.SeqAcnucWeb getTrans.SeqFastadna getTrans.SeqFrag
-[4] getTrans.character getTrans.default getTrans.list
-[7] getTrans.logical getTrans.qaw
+[1] getTrans.character getTrans.default getTrans.list
+[4] getTrans.logical getTrans.qaw getTrans.SeqAcnucWeb
+[7] getTrans.SeqFastadna getTrans.SeqFrag
\end{Soutput}
\begin{Sinput}
methods(getAnnot)
\end{Sinput}
\begin{Soutput}
-[1] getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA getAnnot.SeqFastadna
-[4] getAnnot.default getAnnot.list getAnnot.logical
-[7] getAnnot.qaw
+[1] getAnnot.default getAnnot.list getAnnot.logical
+[4] getAnnot.qaw getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA
+[7] getAnnot.SeqFastadna
\end{Soutput}
\begin{Sinput}
methods(getLocation)
\end{Sinput}
\begin{Soutput}
-[1] getLocation.SeqAcnucWeb getLocation.default getLocation.list
-[4] getLocation.logical getLocation.qaw
+[1] getLocation.default getLocation.list getLocation.logical
+[4] getLocation.qaw getLocation.SeqAcnucWeb
\end{Soutput}
\end{Schunk}
@@ -406,93 +406,63 @@
\clearpage
-\subsection{Sequences as strings}
+%
+% Things are changing with R 2.10, this is no more correct
+%
+%\subsection{Sequences as strings}
+%
+%If you are interested in (fuzzy) pattern matching, then it is advisable to work with
+%sequence as strings to take advantage of \emph{regular expression} implemented
+%in \Rlogo{}. The function \texttt{words.pos()} returns the positions of all occurrences
+%of a given regular expression. Let's suppose we want to know where are the trinucleotides
+%"cgt" in a sequence, that is the fragment CpGpT in the direct strand:
+%
+%<<cgt, eval=T>>=
+%mystring <- c2s(myseq)
+%(cgt <- words.pos("cgt", mystring))
+%substring(mystring, cgt, cgt+2)
+%@
+%
+%We can also look for the fragment CpGpTpY to illustrate fuzzy matching because
+%Y (IUPAC code for pyrimidine) stands C or T:
+%
+%<<fuzzy, eval=T>>=
+%(cgty <- words.pos("cgt[ct]", mystring))
+%substring(mystring, cgty, cgty+3)
+%@
+%
+%To look for all CpC dinucleotides separated by 3 or 4 bases:
+%<<fuzzy2, eval=T>>=
+%(cc34cc <- words.pos("cc.{3,4}cc", mystring, perl = TRUE))
+%substring(mystring, cc34cc, cc34cc+7)
+%@
+%
+%Virtually any pattern is easily encoded with a regular expression. This is
+%especially useful at the protein level because many functions can be attributed
+%to short linear motifs.
-If you are interested in (fuzzy) pattern matching, then it is advisable to work with
-sequence as strings to take advantage of \emph{regular expression} implemented
-in \Rlogo{}. The function \texttt{words.pos()} returns the positions of all occurrences
-of a given regular expression. Let's suppose we want to know where are the trinucleotides
-"cgt" in a sequence, that is the fragment CpGpT in the direct strand:
-\begin{Schunk}
-\begin{Sinput}
- mystring <- c2s(myseq)
- (cgt <- words.pos("cgt", mystring))
-\end{Sinput}
-\begin{Soutput}
- [1] 24 90 216 245 252 315 330 405 432 452 552 592 648 836 883
-\end{Soutput}
-\begin{Sinput}
- substring(mystring, cgt, cgt + 2)
-\end{Sinput}
-\begin{Soutput}
- [1] "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt" "cgt"
-[13] "cgt" "cgt" "cgt"
-\end{Soutput}
-\end{Schunk}
-
-We can also look for the fragment CpGpTpY to illustrate fuzzy matching because
-Y (IUPAC code for pyrimidine) stands C or T:
-
-\begin{Schunk}
-\begin{Sinput}
- (cgty <- words.pos("cgt[ct]", mystring))
-\end{Sinput}
-\begin{Soutput}
- [1] 24 216 252 315 432 452 552 592 836 883
-\end{Soutput}
-\begin{Sinput}
- substring(mystring, cgty, cgty + 3)
-\end{Sinput}
-\begin{Soutput}
- [1] "cgtc" "cgtt" "cgtc" "cgtt" "cgtt" "cgtt" "cgtc" "cgtc" "cgtt" "cgtt"
-\end{Soutput}
-\end{Schunk}
-
-To look for all CpC dinucleotides separated by 3 or 4 bases:
-\begin{Schunk}
-\begin{Sinput}
- (cc34cc <- words.pos("cc.{3,4}cc", mystring, perl = TRUE))
-\end{Sinput}
-\begin{Soutput}
- [1] 72 119 176 177 539 577 578 638 677 682 730 731 736 881 882
-\end{Soutput}
-\begin{Sinput}
- substring(mystring, cc34cc, cc34cc + 7)
-\end{Sinput}
-\begin{Soutput}
- [1] "ccttgccg" "ccattcca" "cccagacc" "ccagacca" "cctatgcc" "cccgatcc"
- [7] "ccgatccg" "ccagctcc" "ccgctcca" "ccagctcc" "cccgctcc" "ccgctccg"
-[13] "ccggcacc" "cccgttcc" "ccgttcca"
-\end{Soutput}
-\end{Schunk}
-
-Virtually any pattern is easily encoded with a regular expression. This is
-especially useful at the protein level because many functions can be attributed
-to short linear motifs.
-
-
\section*{Session Informations}
\begin{scriptsize}
This part was compiled under the following \Rlogo{}~environment:
-\begin{itemize}
- \item R version 2.9.0 (2009-04-17), \verb|i386-apple-darwin8.11.1|
- \item Locale: \verb|C|
- \item Base packages: base, datasets, grDevices, graphics, grid,
+\begin{itemize}\raggedright
+ \item R version 2.10.0 (2009-10-26), \verb|i386-apple-darwin8.11.1|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \item Other packages: MASS~7.2-46, XML~2.3-0, ade4~1.4-11,
- ape~2.3, grImport~0.4-3, quadprog~1.4-11, seqinr~2.0-3,
- tseries~0.10-18, xtable~1.5-5, zoo~1.5-5
- \item Loaded via a namespace (and not attached): gee~4.13-13,
- lattice~0.17-22, nlme~3.1-90, tools~2.9.0
+ \item Other packages: ade4~1.4-13, ape~2.4, grImport~0.4-4,
+ MASS~7.3-3, quadprog~1.4-11, seqinr~2.0-7, tseries~0.10-21,
+ XML~2.6-0, xtable~1.5-5, zoo~1.5-8
+ \item Loaded via a namespace (and not attached): gee~4.13-14,
+ lattice~0.17-26, nlme~3.1-96, tools~2.10.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Apr 23 11:52:14 2009
+ \item \Rlogo{} compilation time was: Thu Nov 5 14:18:57 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
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