[Seqinr-commits] r1859 - www/src/appendix
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 1 17:14:25 CEST 2016
Author: jeanlobry
Date: 2016-06-01 17:14:25 +0200 (Wed, 01 Jun 2016)
New Revision: 1859
Modified:
www/src/appendix/FAQ.rnw
www/src/appendix/FAQ.tex
Log:
query bugs fixed now
Modified: www/src/appendix/FAQ.rnw
===================================================================
--- www/src/appendix/FAQ.rnw 2016-06-01 14:50:22 UTC (rev 1858)
+++ www/src/appendix/FAQ.rnw 2016-06-01 15:14:25 UTC (rev 1859)
@@ -5,6 +5,7 @@
\author{Lobry, J.R.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
% BEGIN - DO NOT REMOVE THIS LINE
@@ -94,7 +95,7 @@
}
@
-The following code\footnote{
+The following code\footnote{%
This code is adapted from the code at \url{http://www.stat.auckland.ac.nz/~paul/RGraphics/chapter3.html} for
figure 3.25 in Paul Murrell's book \cite{MurrellP2005}. This book is a must read if you are interested
by \Rlogo{}'s \textit{force de frappe} in the graphic domain.
@@ -180,7 +181,7 @@
<<getFrag,fig=F>>=
choosebank("emblTP")
-query("mylist", "AC=A00001")
+mylist <- query("mylist", "AC=A00001")
getFrag(mylist$req[[1]], begin = 10, end = 20)
closebank()
@
@@ -192,7 +193,7 @@
<<gc3, fig=F,eval=T>>=
choosebank("emblTP")
-query("ecribo","sp=escherichia coli ET t=cds ET k=ribosom@ ET NO k=partial")
+ecribo <- query("ecribo","sp=escherichia coli ET t=cds ET k=ribosom@ ET NO k=partial")
myseqs <- sapply(ecribo$req, getSequence)
(gc3 <- sapply(myseqs, GC3))
@
@@ -365,14 +366,14 @@
This question is adapted from an e-mail (22 Jun 2006) by Gang Xu.
I know that the UniProt (SwissProt) entry of my protein is \texttt{P08758},
-if I know its name\footnote{
+if I know its name\footnote{%
More exactly, this is the accession number. Sequence names are not stable over time,
it's always better to use the accession numbers.
}, how can I get the sequence?
<<uniprot,fig=F,eval=T>>=
choosebank("swissprot")
-query("myprot","AC=P08758")
+myprot <- query("myprot","AC=P08758")
getSequence(myprot$req[[1]])
@
Modified: www/src/appendix/FAQ.tex
===================================================================
--- www/src/appendix/FAQ.tex 2016-06-01 14:50:22 UTC (rev 1858)
+++ www/src/appendix/FAQ.tex 2016-06-01 15:14:25 UTC (rev 1859)
@@ -6,6 +6,7 @@
\usepackage{Sweave}
\begin{document}
+\input{FAQ-concordance}
%
% To change the R input/output style:
%
@@ -93,15 +94,13 @@
\begin{Schunk}
\begin{Sinput}
- gcskew <- function(x) {
- if (!is.character(x) || length(x) > 1)
- stop("single string expected")
- tmp <- tolower(s2c(x))
- nC <- sum(tmp == "c")
- nG <- sum(tmp == "g")
- if (nC + nG == 0)
- return(NA)
- return(100 * (nC - nG)/(nC + nG))
+ gcskew <- function(x){
+ if( !is.character(x) || length(x) > 1 ) stop("single string expected")
+ tmp <- tolower(s2c(x))
+ nC <- sum(tmp == "c")
+ nG <- sum(tmp == "g")
+ if( nC + nG == 0 ) return(NA)
+ return(100*(nC - nG)/(nC + nG))
}
gcskew("GCCC")
\end{Sinput}
@@ -137,17 +136,16 @@
step <- 10000
wsize <- 10000
starts <- seq(from = 1, to = nchar(myseq), by = step)
- starts <- starts[-length(starts)]
+ starts <- starts[-length(starts)] # remove last one
n <- length(starts)
result <- numeric(n)
- for (i in seq_len(n)) {
- result[i] <- gcskew(substr(myseq, starts[i], starts[i] +
- wsize - 1))
+ for(i in seq_len(n)){
+ result[i] <- gcskew(substr(myseq, starts[i], starts[i] + wsize - 1))
}
\end{Sinput}
\end{Schunk}
-The following code\footnote{
+The following code\footnote{%
This code is adapted from the code at \url{http://www.stat.auckland.ac.nz/~paul/RGraphics/chapter3.html} for
figure 3.25 in Paul Murrell's book \cite{MurrellP2005}. This book is a must read if you are interested
by \Rlogo{}'s \textit{force de frappe} in the graphic domain.
@@ -159,19 +157,17 @@
yy <- result
n <- length(result)
hline <- 0
- plot(yy ~ xx, type = "n", axes = FALSE, ann = FALSE, ylim = c(-10,
- 10))
- polygon(c(xx[1], xx, xx[n]), c(min(yy), yy, min(yy)), col = "black",
- border = NA)
+ plot (yy ~ xx, type="n", axes=FALSE, ann=FALSE, ylim = c(-10, 10))
+ polygon(c(xx[1], xx, xx[n]), c(min(yy), yy, min(yy)), col = "black", border=NA)
usr <- par("usr")
- rect(usr[1], usr[3], usr[2], hline, col = "white", border = NA)
+ rect(usr[1], usr[3], usr[2], hline, col="white", border=NA)
lines(xx, yy)
- abline(h = hline)
+ abline (h=hline)
box()
- axis(1, at = seq(0, 1600, by = 200))
- axis(2, las = 1)
- title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) %", main = expression(paste("GC skew in ",
- italic(Escherichia ~ ~coli))))
+ axis(1, at = seq(0,1600, by = 200))
+ axis(2, las = 1)
+ title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) %",
+ main = expression(paste("GC skew in ", italic(Escherichia~~coli))))
arrows(860, 5.5, 720, 0.5, length = 0.1, lwd = 2)
text(860, 5.5, "origin of replication", pos = 4)
\end{Sinput}
@@ -198,21 +194,17 @@
\begin{Schunk}
\begin{Sinput}
- plot(xx, yy, col = "grey", type = "b", ylim = c(-10, 10),
- las = 1, xaxt = "n", main = expression(paste("GC skew in ",
- italic(Escherichia ~ ~coli))), xlab = "position (Kbp)",
- ylab = "(C-G)/(C+G) %")
- axis(1, at = seq(0, 1600, by = 200))
- lines(smooth <- lowess(xx, yy, f = 0.05), lwd = 1)
- polycurve <- function(x, y, base.y = min(y), ...) polygon(x = c(min(x),
- x, max(x)), y = c(base.y, y, base.y), ...)
+ plot(xx,yy, col = "grey", type = "b", ylim = c(-10,10), las = 1, xaxt = "n",
+ main = expression(paste("GC skew in ", italic(Escherichia~~coli))),
+ xlab = "position (Kbp)", ylab = "(C-G)/(C+G) %")
+ axis(1, at = seq(0,1600, by = 200))
+ lines(smooth <- lowess(xx,yy, f = 0.05), lwd = 1)
+ polycurve <- function(x, y, base.y = min(y), ...) polygon(x = c(min(x), x, max(x)), y = c(base.y, y, base.y), ...)
up <- smooth$y > 0
- polycurve(smooth$x[up], smooth$y[up], base.y = 0, col = rgb(0,
- 0, 1, 0.5))
- lines(lowess(xx, yy, f = 0.2), lwd = 2, col = "red")
- legend("topright", inset = 0.01, legend = c("f = 0.05", "f = 0.20"),
- lwd = c(1, 2), col = c("black", "red"))
- abline(h = 0)
+ polycurve(smooth$x[up], smooth$y[up], base.y = 0, col = rgb(0,0,1,0.5))
+ lines(lowess(xx,yy, f = 0.2), lwd = 2, col = "red")
+ legend("topright", inset = 0.01, legend = c("f = 0.05", "f = 0.20"), lwd = c(1,2), col = c("black", "red"))
+ abline(h=0)
arrows(860, 5.5, 720, 0.5, length = 0.1, lwd = 2)
text(860, 5.5, "origin of replication", pos = 4)
\end{Sinput}
@@ -238,7 +230,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("mylist", "AC=A00001")
+ mylist <- query("mylist", "AC=A00001")
getFrag(mylist$req[[1]], begin = 10, end = 20)
\end{Sinput}
\begin{Soutput}
@@ -265,7 +257,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ecribo", "sp=escherichia coli ET t=cds ET k=ribosom@ ET NO k=partial")
+ ecribo <- query("ecribo","sp=escherichia coli ET t=cds ET k=ribosom@ ET NO k=partial")
myseqs <- sapply(ecribo$req, getSequence)
(gc3 <- sapply(myseqs, GC3))
\end{Sinput}
@@ -288,17 +280,17 @@
\begin{Schunk}
\begin{Sinput}
- sapply(sapply(myseqs, getTrans), computePI)
+ sapply( sapply(myseqs, getTrans), computePI)
\end{Sinput}
\begin{Soutput}
[1] 6.624309 7.801329 10.864793 5.931989 7.830476 6.624309 7.801329
[8] 9.203410 9.826485 5.674672 7.154423 6.060457 6.313741 5.571446
-[15] 9.435422 4.310745 6.145496 4.876054 11.006430 10.876041 6.624309
+[15] 9.435422 4.310747 6.145496 4.876054 11.006430 10.876041 6.624309
[22] 7.801329 10.864793 9.346289 9.203410 5.877050 5.931989 9.934988
[29] 5.920490 6.612505 6.624309 6.624309 7.801329 10.864793 5.931989
[36] 11.182505 9.598944 6.624309 10.864793 9.203410 11.031938 5.858421
-[43] 5.858421 11.777511 11.777511 10.619175 11.365738 9.460987 10.864793
-[50] 13.002381 9.845859 10.584868 11.421252 10.248325 11.031943 10.402075
+[43] 5.858421 11.777516 11.777511 10.619175 11.365738 9.460987 10.864793
+[50] 13.002373 9.845859 10.584868 11.421252 10.248320 11.031943 10.402075
[57] 4.863862 6.612505 9.681066 11.150310 11.182505 11.043607 6.624309
[64] 6.612505 6.624309 4.310747
\end{Soutput}
@@ -312,8 +304,7 @@
\begin{Schunk}
\begin{Sinput}
- GC3m <- function(list, ind = 1:list$nelem) sapply(sapply(list$req[ind],
- getSequence), GC3)
+ GC3m <- function(list, ind = 1:list$nelem) sapply(sapply(list$req[ind], getSequence), GC3)
GC3m(ecribo)
\end{Sinput}
\begin{Soutput}
@@ -348,8 +339,7 @@
\begin{Schunk}
\begin{Sinput}
- gc3nos <- sapply(myseqs, function(s) GC3(s[1:(length(s) -
- 3)]))
+ gc3nos <- sapply(myseqs, function(s) GC3(s[1:(length(s) - 3)]))
\end{Sinput}
\end{Schunk}
@@ -357,9 +347,9 @@
\begin{Schunk}
\begin{Sinput}
- plot(x = gc3, y = gc3nos, las = 1, main = "Stop codon removal effect on G+C content\nin third codon positions",
- xlab = "With stop codon", ylab = "Stop codons removed")
- abline(c(0, 1))
+ plot(x = gc3, y = gc3nos, las =1, main="Stop codon removal effect on G+C content
+ in third codon positions", xlab = "With stop codon", ylab ="Stop codons removed")
+ abline(c(0,1))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/FAQ-stopcodonremovaleffect}
@@ -370,7 +360,7 @@
\begin{Schunk}
\begin{Sinput}
inputdatfile <- system.file("sequences/input.dat", package = "seqinr")
- cat(readLines(inputdatfile, n = 10), sep = "\n")
+ cat(readLines(inputdatfile,n=10), sep = "\n")
\end{Sinput}
\begin{Soutput}
>YCG9 Probable 1377 residues Pha 0 Code 0
@@ -422,7 +412,7 @@
\begin{Schunk}
\begin{Sinput}
inputoutfile <- system.file("sequences/input.out", package = "seqinr")
- cat(readLines(inputoutfile, n = 10), sep = "\n")
+ cat(readLines(inputoutfile, n=10), sep = "\n")
\end{Sinput}
\begin{Soutput}
title GC3s GC
@@ -456,17 +446,17 @@
\begin{Schunk}
\begin{Sinput}
- input.gc <- sapply(input, function(s) GC(s[1:(length(s) -
- 3)]))
+ input.gc <- sapply(input, function(s) GC(s[1:(length(s)-3)]))
max(abs(input.gc - input.res$GC))
\end{Sinput}
\begin{Soutput}
[1] 0.0004946237
\end{Soutput}
\begin{Sinput}
- plot(x = input.gc, y = input.res$GC, las = 1, xlab = "Results with GC()",
- ylab = "Results from codonW", main = "Comparison of G+C content results")
- abline(c(0, 1))
+ plot(x = input.gc, y = input.res$GC, las = 1,
+ xlab = "Results with GC()", ylab = "Results from codonW",
+ main = "Comparison of G+C content results")
+ abline(c(0,1))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/FAQ-inputgc}
@@ -477,17 +467,17 @@
\begin{Schunk}
\begin{Sinput}
- input.gc3 <- sapply(input, function(s) GC3(s[1:(length(s) -
- 3)]))
+ input.gc3 <- sapply(input, function(s) GC3(s[1:(length(s)-3)]))
max(abs(input.gc3 - input.res$GC3s))
\end{Sinput}
\begin{Soutput}
[1] 0.054
\end{Soutput}
\begin{Sinput}
- plot(x = input.gc3, y = input.res$GC3s, las = 1, xlab = "Results with GC3()",
- ylab = "Results from codonW", main = "Comparison of G+C content in third codon positions results")
- abline(c(0, 1))
+ plot(x = input.gc3, y = input.res$GC3s, las = 1,
+ xlab = "Results with GC3()", ylab = "Results from codonW",
+ main = "Comparison of G+C content in third codon positions results")
+ abline(c(0,1))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/FAQ-inputgc3}
@@ -500,14 +490,13 @@
\begin{Schunk}
\begin{Sinput}
codons <- words()
- names(codons) <- sapply(codons, function(c) aaa(translate(s2c(c),
- numcode = 1)))
- okcodons <- codons[!names(codons) %in% c("Met", "Trp", "Stp")]
- gc3s <- function(s) {
- tmp <- splitseq(s)
- tmp <- tmp[tmp %in% okcodons]
- tmp <- s2c(paste(tmp, collapse = ""))
- GC3(tmp)
+ names(codons) <- sapply(codons, function(c) aaa(translate(s2c(c), numcode = 1)))
+ okcodons <- codons[! names(codons) %in% c("Met", "Trp", "Stp")]
+ gc3s <- function(s){
+ tmp <- splitseq(s)
+ tmp <- tmp[tmp %in% okcodons]
+ tmp <- s2c(paste(tmp, collapse = ""))
+ GC3(tmp)
}
input.gc3s <- sapply(input, gc3s)
max(abs(input.gc3s - input.res$GC3s))
@@ -516,9 +505,10 @@
[1] 0.0004980843
\end{Soutput}
\begin{Sinput}
- plot(x = input.gc3s, y = input.res$GC3s, las = 1, xlab = "Results with GC3()",
- ylab = "Results from codonW", main = "Comparison of G+C content in third codon positions results\n(Met, Trp and Stp codons excluded)")
- abline(c(0, 1))
+ plot(x = input.gc3s, y = input.res$GC3s, las = 1,
+ xlab = "Results with GC3()", ylab = "Results from codonW",
+ main = "Comparison of G+C content in third codon positions results\n(Met, Trp and Stp codons excluded)")
+ abline(c(0,1))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/FAQ-inputgc3s}
@@ -560,13 +550,12 @@
\begin{Schunk}
\begin{Sinput}
- P3codons <- codons[!names(codons) %in% c("Met", "Trp", "Ile",
- "Stp")]
- P3 <- function(s) {
- tmp <- splitseq(s)
- tmp <- tmp[tmp %in% P3codons]
- tmp <- s2c(paste(tmp, collapse = ""))
- GC3(tmp)
+ P3codons <- codons[! names(codons) %in% c("Met", "Trp", "Ile", "Stp")]
+ P3 <- function(s){
+ tmp <- splitseq(s)
+ tmp <- tmp[tmp %in% P3codons]
+ tmp <- s2c(paste(tmp, collapse = ""))
+ GC3(tmp)
}
input.P3 <- sapply(input, P3)
max(abs(input.P3 - input.res$GC3s))
@@ -575,9 +564,10 @@
[1] 0.02821505
\end{Soutput}
\begin{Sinput}
- plot(x = input.P3, y = input.res$GC3s, las = 1, xlab = "Results with P3",
- ylab = "Results from codonW GC3s", main = "Comparison of P3 and GC3s")
- abline(c(0, 1))
+ plot(x = input.P3, y = input.res$GC3s, las = 1,
+ xlab = "Results with P3", ylab = "Results from codonW GC3s",
+ main = "Comparison of P3 and GC3s")
+ abline(c(0,1))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/FAQ-inputP3}
@@ -589,16 +579,16 @@
This question is adapted from an e-mail (22 Jun 2006) by Gang Xu.
I know that the UniProt (SwissProt) entry of my protein is \texttt{P08758},
-if I know its name\footnote{
+if I know its name\footnote{%
More exactly, this is the accession number. Sequence names are not stable over time,
it's always better to use the accession numbers.
}, how can I get the sequence?
\begin{Schunk}
\begin{Sinput}
- choosebank("swissprot")
- query("myprot", "AC=P08758")
- getSequence(myprot$req[[1]])
+ choosebank("swissprot")
+ myprot <- query("myprot","AC=P08758")
+ getSequence(myprot$req[[1]])
\end{Sinput}
\begin{Soutput}
[1] "M" "A" "Q" "V" "L" "R" "G" "T" "V" "T" "D" "F" "P" "G" "F" "D" "E" "R"
@@ -630,20 +620,20 @@
This part was compiled under the following \Rlogo{}~environment:
\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 R version 3.2.4 (2016-03-10), \verb|x86_64-apple-darwin13.4.0|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8|
\item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \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
+ \item Other packages: ade4~1.7-4, ape~3.5, grImport~0.9-0,
+ MASS~7.3-45, seqinr~3.1-5, tseries~0.10-35, XML~3.98-1.4,
+ xtable~1.8-2
+ \item Loaded via a namespace (and not attached): lattice~0.20-33,
+ nlme~3.1-125, quadprog~1.5-5, tools~3.2.4, zoo~1.7-12
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Nov 5 14:57:01 2009
+ \item \Rlogo{} compilation time was: Wed Jun 1 17:13:01 2016
\item \LaTeX{} compilation time was: \today
\end{itemize}
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