[Seqinr-commits] r1692 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 5 14:49:00 CET 2009
Author: lobry
Date: 2009-11-05 14:48:59 +0100 (Thu, 05 Nov 2009)
New Revision: 1692
Modified:
pkg/inst/doc/src/mainmatter/nonparastats.rnw
pkg/inst/doc/src/mainmatter/nonparastats.tex
Log:
compil R 2.10
Modified: pkg/inst/doc/src/mainmatter/nonparastats.rnw
===================================================================
--- pkg/inst/doc/src/mainmatter/nonparastats.rnw 2009-11-05 13:27:02 UTC (rev 1691)
+++ pkg/inst/doc/src/mainmatter/nonparastats.rnw 2009-11-05 13:48:59 UTC (rev 1692)
@@ -60,7 +60,7 @@
%
% Data saved in *.RData format to avoid long computation
%
-<<getdatafomensemble,fig=F,eval=TRUE>>=
+<<getdatafomensemble,fig=F,eval=FALSE>>=
choosebank("ensembl")
n <- 201
res <- rep(-1,10*n)
@@ -540,12 +540,17 @@
chromosome from the Genome Reviews database. Let's use, for instance,
the following CDS:
-<<querycds,fig=F,eval=T>>=
-choosebank("greview")
-query("coli","N=U00096 ET T=CDS ET K=2.3.1.79@")
+<<querycds,fig=F,eval=F>>=
+choosebank("greviews")
+query("coli","N=U00096_GR ET T=CDS ET K=2.3.1.79@")
sequence <- getSequence(coli$req[[1]])
annot <- getAnnot(coli$req[[1]])
closebank()
+save(sequence, file = "sequence.RData")
+save(annot, file = "annot.RData")
+@
+<<showannot,fig=F,eval=T>>=
+load("annot.RData")
cat(annot, sep="\n")
@
@@ -572,6 +577,7 @@
code was used to produce figure \ref{dinuclcoli}:
<<dinuclcoli, echo = TRUE, fig = TRUE,include=F,eval=T>>=
+load("sequence.RData")
rhocoli <- rho(sequence)
zcolibase <- zscore(sequence, model = 'base', exact = TRUE)
zcolicodon <- zscore(sequence,model = 'codon', exact = TRUE)
Modified: pkg/inst/doc/src/mainmatter/nonparastats.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/nonparastats.tex 2009-11-05 13:27:02 UTC (rev 1691)
+++ pkg/inst/doc/src/mainmatter/nonparastats.tex 2009-11-05 13:48:59 UTC (rev 1692)
@@ -754,40 +754,51 @@
\begin{Schunk}
\begin{Sinput}
- choosebank("greview")
- query("coli", "N=U00096 ET T=CDS ET K=2.3.1.79@")
+ choosebank("greviews")
+ query("coli", "N=U00096_GR ET T=CDS ET K=2.3.1.79@")
sequence <- getSequence(coli$req[[1]])
annot <- getAnnot(coli$req[[1]])
closebank()
+ save(sequence, file = "sequence.RData")
+ save(annot, file = "annot.RData")
+\end{Sinput}
+\end{Schunk}
+\begin{Schunk}
+\begin{Sinput}
+ load("annot.RData")
cat(annot, sep = "\n")
\end{Sinput}
\begin{Soutput}
FT CDS complement(478591..479142)
FT /codon_start=1
-FT /gene="maa {UniProt/Swiss-Prot:P77791}"
-FT /locus_tag="b0459 {UniProt/Swiss-Prot:P77791}"
-FT /product="Maltose O-acetyltransferase
-FT {UniProt/Swiss-Prot:P77791}"
-FT /EC_number="2.3.1.79 {UniProt/Swiss-Prot:P77791}"
-FT /function="maltose O-acetyltransferase activity
+FT /evidence="1: Evidence at protein level
+FT {UniProtKB/Swiss-Prot:P77791}"
+FT /gene_id="IGI00122745"
+FT /gene_name="maa {UniProtKB/Swiss-Prot:P77791}"
+FT /gene_synonym="ECK0453"
+FT /gene_synonym="ylaD {UniProtKB/Swiss-Prot:P77791}"
+FT /locus_tag="b0459 {UniProtKB/Swiss-Prot:P77791}"
+FT /product="Maltose O-acetyltransferase
+FT {UniProtKB/Swiss-Prot:P77791}"
+FT /EC_number="2.3.1.79 {UniProtKB/Swiss-Prot:P77791}"
+FT /function="maltose O-acetyltransferase activity
FT {GO:0008925}"
FT /protein_id="AAC73561.1 {EMBL:U00096}"
-FT /db_xref="EMBL:AAB40214.1 {UniProt/Swiss-Prot:P77791}"
-FT /db_xref="EMBL:CAA11147.1 {UniProt/Swiss-Prot:P77791}"
-FT /db_xref="EcoGene:EG14239 {UniProt/Swiss-Prot:P77791}"
+FT /db_xref="EMBL:AAB40214.1 {UniProtKB/Swiss-Prot:P77791}"
+FT /db_xref="EMBL:CAA11147.1 {UniProtKB/Swiss-Prot:P77791}"
+FT /db_xref="EcoGene:EG14239 {UniProtKB/Swiss-Prot:P77791}"
FT /db_xref="GO:0008925 {GOA:P77791}"
-FT /db_xref="HOGENOM:HBG023156 {HogenProt:P77791}"
-FT /db_xref="InterPro:IPR001451 {UniProt/Swiss-Prot:P77791}"
-FT /db_xref="InterPro:IPR011004 {UniProt/Swiss-Prot:P77791}"
+FT /db_xref="HOGENOM:HBG282173 {HogenProt:P77791}"
+FT /db_xref="HOGENOM:P77791 {UniProtKB/Swiss-Prot:P77791}"
+FT /db_xref="InterPro:IPR001451 {UniProtKB/Swiss-Prot:P77791}"
+FT /db_xref="PDB:1OCX {UniProtKB/Swiss-Prot:P77791}"
FT /db_xref="UniParc:UPI000002EA96 {EMBL:AAC73561}"
-FT /db_xref="UniProt/Swiss-Prot:P77791 {EMBL:U00096}"
+FT /db_xref="UniProtKB/Swiss-Prot:P77791 {EMBL:U00096}"
FT /transl_table=11
FT /translation="MSTEKEKMIAGELYRSADETLSRDRLRARQLIHRYNHSLAEEHTL
FT RQQILADLFGQVTEAYIEPTFRCDYGYNIFLGNNFFANFDCVMLDVCPIRIGDNCMLAP
FT GVHIYTATHPIDPVARNSGAELGKPVTIGNNVWIGGRAVINPGVTIGDNVVVASGAVVT
FT KDVPDNVVVGGNPARIIKKL"
-FT /%(C+G)="CG<50%"
-FT /note="C+G content in third codon positions = 47.8 % "
\end{Soutput}
\end{Schunk}
@@ -815,6 +826,7 @@
\begin{Schunk}
\begin{Sinput}
+ load("sequence.RData")
rhocoli <- rho(sequence)
zcolibase <- zscore(sequence, model = "base", exact = TRUE)
zcolicodon <- zscore(sequence, model = "codon", exact = TRUE)
@@ -1292,21 +1304,21 @@
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|
- \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 12:01:42 2009
+ \item \Rlogo{} compilation time was: Thu Nov 5 14:48:01 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
More information about the Seqinr-commits
mailing list