[Seqinr-commits] r1685 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 5 12:54:45 CET 2009
Author: lobry
Date: 2009-11-05 12:54:45 +0100 (Thu, 05 Nov 2009)
New Revision: 1685
Modified:
pkg/inst/doc/src/mainmatter/getseqacnuc.tex
Log:
compil R 2.10
Modified: pkg/inst/doc/src/mainmatter/getseqacnuc.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2009-11-05 11:54:14 UTC (rev 1684)
+++ pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2009-11-05 11:54:45 UTC (rev 1685)
@@ -75,14 +75,17 @@
choosebank()
\end{Sinput}
\begin{Soutput}
- [1] "genbank" "embl" "emblwgs" "swissprot"
- [5] "ensembl" "refseq" "nrsub" "hobacnucl"
- [9] "hobacprot" "hovergendna" "hovergen" "hogenom"
-[13] "hogenomdna" "hogennucl" "hogenprot" "hoverclnu"
-[17] "hoverclpr" "homolens3" "homolens3dna" "homolens"
-[21] "homolensdna" "greview" "polymorphix" "emglib"
-[25] "HAMAPnucl" "HAMAPprot" "taxobacgen" "apis"
-[29] "human"
+ [1] "genbank" "embl" "emblwgs" "swissprot"
+ [5] "ensembl" "refseq" "refseqViruses" "nrsub"
+ [9] "hobacnucl" "hobacprot" "hovergendna" "hovergen"
+[13] "hogenom5" "hogenom5dna" "hogenom" "hogenomdna"
+[17] "hogennucl" "hogenprot" "hoverclnu" "hoverclpr"
+[21] "homolens3" "homolens3dna" "homolens" "homolensdna"
+[25] "greviews" "polymorphix" "emglib" "HAMAPnucl"
+[29] "HAMAPprot" "taxobacgen" "apis" "anopheles"
+[33] "caenorhabditis" "ciona_savignyi" "danio" "drosophila"
+[37] "felis" "gallus" "human" "mouse"
+[41] "saccharomyces" "tetraodon" "xenopus"
\end{Soutput}
\end{Schunk}
@@ -103,10 +106,10 @@
1 genbank on
2 embl on
3 emblwgs on
- info
-1 GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009
-2 EMBL Library Release 99 (March 2009) Last Updated: Apr 23, 2009
-3 EMBL Whole Genome Shotgun sequences Release 99 (March 2009)
+ info
+1 GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009
+2 EMBL Library Release 101 (September 2009) Last Updated: Nov 5, 2009
+3 EMBL Whole Genome Shotgun sequences Release 101 (September 2009)
\end{Soutput}
\end{Schunk}
@@ -164,12 +167,12 @@
.. ..- attr(*, "conn_id")=<externalptr>
$ bankname: chr "genbank"
$ banktype: chr "GENBANK"
- $ totseqs : num 1.1e+08
- $ totspecs: num 637489
- $ totkeys : num 13783816
- $ release : chr " GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009"
+ $ totseqs : num 1.19e+08
+ $ totspecs: num 686783
+ $ totkeys : num 15791073
+ $ release : chr " GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009"
$ status :Class 'AsIs' chr "on"
- $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009" "103,287,086,629 bases; 103,570,547 sequences; 6,354,023 subseqs; 549,786 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
+ $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009" "108,943,317,873 bases; 111,355,981 sequences; 7,239,424 subseqs; 573,990 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
\end{Soutput}
\begin{Sinput}
closebank()
@@ -179,15 +182,15 @@
The components of \texttt{banknameSocket} means that in the database
called \texttt{genbank} at the compilation time
of this document there were
-\texttt{109,924,571}
+\texttt{118,595,406}
sequences from
-\texttt{637,489}
+\texttt{686,783}
species and a total of
-\texttt{13,783,816}
+\texttt{15,791,073}
keywords. The status of the bank was
\texttt{on},
and the release information was
-\texttt{ GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009}.
+\texttt{ GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009}.
For specialized databases, some relevant informations are also given in the
\texttt{details} component, for instance:
@@ -311,9 +314,9 @@
getName(completeCatsCDS$req[1:10])
\end{Sinput}
\begin{Soutput}
- [1] "AB000483.PE1" "AB000484.PE1" "AB000485.PE1" "AB004237"
- [5] "AB004238" "AB009279.PE1" "AB009280.PE1" "AB010872.UGT1A1"
- [9] "AB011965.SDF-1A" "AB011966.SDF-1B"
+ [1] "AB000483.PE1" "AB000484.PE1" "AB000485.PE1" "AB003366"
+ [5] "AB003367" "AB004237" "AB004238" "AB009279.PE1"
+ [9] "AB009280.PE1" "AB010872.UGT1A1"
\end{Soutput}
\end{Schunk}
@@ -383,15 +386,15 @@
allcds$nelem
\end{Sinput}
\begin{Soutput}
-[1] 6900945
+[1] 7992598
\end{Soutput}
\end{Schunk}
-There are therefore \texttt{6,900,945} coding
+There are therefore \texttt{7,992,598} coding
sequences in this version of GenBank\footnote{
which is stored in the \texttt{release} component of the object \texttt{banknameSocket}
and current value is today (\today): \texttt{banknameSocket\$release =
- GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009}.
+ GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009}.
}.
It would be long to get all the informations for the elements
of this list, so we have set the parameter \texttt{virtual} to \texttt{TRUE} and the \texttt{req}
@@ -418,11 +421,11 @@
small$nelem
\end{Sinput}
\begin{Soutput}
-[1] 956
+[1] 979
\end{Soutput}
\end{Schunk}
-There are then \texttt{956} elements in
+There are then \texttt{979} elements in
the list \texttt{small}, so that we can safely repeat the previous query without asking for a
virtual list:
@@ -448,10 +451,10 @@
man$nelem
\end{Sinput}
\begin{Soutput}
-[1] 12404202
+[1] 13042724
\end{Soutput}
\end{Schunk}
-There are \texttt{12,404,202} sequences from \textit{Homo sapiens}.
+There are \texttt{13,042,724} sequences from \textit{Homo sapiens}.
\item[\textbf{Sex.}] How many sequences are annotated with a keyword starting by sex?
\begin{Schunk}
@@ -460,10 +463,10 @@
sex$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1397
+[1] 1465
\end{Soutput}
\end{Schunk}
-There are \texttt{1,397} such sequences.
+There are \texttt{1,465} such sequences.
\item[\textbf{tRNA.}] How many complete tRNA sequences are available?
\begin{Schunk}
@@ -472,10 +475,10 @@
trna$nelem
\end{Sinput}
\begin{Soutput}
-[1] 358411
+[1] 413347
\end{Soutput}
\end{Schunk}
-There are \texttt{358,411} complete tRNA sequences.
+There are \texttt{413,347} complete tRNA sequences.
\item[\textbf{Nature vs. Science.}] In which journal were the more sequences published?
\begin{Schunk}
@@ -484,19 +487,19 @@
nature$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1954774
+[1] 1992670
\end{Soutput}
\begin{Sinput}
query("science", "j=science", virtual = T)
science$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1341474
+[1] 1530942
\end{Soutput}
\end{Schunk}
-There are \texttt{1,954,774} sequences published
+There are \texttt{1,992,670} sequences published
in \textit{Nature} and
-\texttt{1,341,474} sequences published in
+\texttt{1,530,942} sequences published in
\textit{Science}, so that the winner is
\textit{Nature}.
@@ -511,10 +514,10 @@
smith$nelem
\end{Sinput}
\begin{Soutput}
-[1] 4754303
+[1] 4809459
\end{Soutput}
\end{Schunk}
-There are \texttt{4,754,303} such sequences.
+There are \texttt{4,809,459} such sequences.
\item[\textbf{YK2.}] How many sequences were published after year 2000 (included)?
\begin{Schunk}
@@ -523,10 +526,10 @@
yk2$nelem
\end{Sinput}
\begin{Soutput}
-[1] 91981106
+[1] 99752843
\end{Soutput}
\end{Schunk}
-There are \texttt{91,981,106} sequences published after year 2000.
+There are \texttt{99,752,843} sequences published after year 2000.
\item[\textbf{Organelle contest.}] Do we have more sequences from chloroplast genomes or from mitochondion genomes?
\begin{Schunk}
@@ -535,19 +538,19 @@
chloro$nelem
\end{Sinput}
\begin{Soutput}
-[1] 223109
+[1] 255832
\end{Soutput}
\begin{Sinput}
query("mito", "o=mitochondrion", virtual = T)
mito$nelem
\end{Sinput}
\begin{Soutput}
-[1] 721261
+[1] 815726
\end{Soutput}
\end{Schunk}
-There are \texttt{223,109} sequences from
+There are \texttt{255,832} sequences from
chloroplast genomes and
-\texttt{721,261} sequences from mitochondrion
+\texttt{815,726} sequences from mitochondrion
genomes, so that the winner is
mitochondrion.
@@ -851,21 +854,21 @@
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|
+\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: ade4~1.4-11, ape~2.3, grImport~0.4-3,
- MASS~7.2-46, quadprog~1.4-11, seqinr~2.0-3, tseries~0.10-18,
- XML~2.3-0, 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 11:29:00 2009
+ \item \Rlogo{} compilation time was: Thu Nov 5 12:36:14 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
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