[Seqinr-commits] r1816 - in pkg: . R data man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 5 17:53:59 CET 2014
Author: simonpenel
Date: 2014-11-05 17:53:58 +0100 (Wed, 05 Nov 2014)
New Revision: 1816
Added:
pkg/data/sysdata.rda
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/AAstat.R
pkg/R/autosocket.R
pkg/R/choosebank.R
pkg/R/extract.breakpoints.R
pkg/R/gb2fasta.R
pkg/R/modifylist.R
pkg/R/oriloc.R
pkg/R/plotabif.R
pkg/R/plotladder.R
pkg/R/query.r
pkg/man/AAstat.Rd
pkg/man/GC.Rd
pkg/man/SEQINR.UTIL.Rd
pkg/man/acnucopen.Rd
pkg/man/as.matrix.alignment.Rd
pkg/man/col2alpha.Rd
pkg/man/computePI.Rd
pkg/man/count.Rd
pkg/man/crelistfromclientdata.Rd
pkg/man/dinucl.Rd
pkg/man/dotPlot.Rd
pkg/man/draw.rearranged.oriloc.Rd
pkg/man/extract.breakpoints.Rd
pkg/man/extractseqs.Rd
pkg/man/gb2fasta.Rd
pkg/man/get.db.growth.Rd
pkg/man/getTrans.Rd
pkg/man/ghelp.Rd
pkg/man/kaks.Rd
pkg/man/m16j.Rd
pkg/man/modifylist.Rd
pkg/man/permutation.Rd
pkg/man/query.Rd
pkg/man/read.abif.Rd
pkg/man/read.alignment.Rd
pkg/man/rearranged.oriloc.Rd
pkg/man/savelist.Rd
pkg/man/stutterabif.Rd
pkg/man/trimSpace.Rd
pkg/man/words.Rd
pkg/man/zscore.Rd
Log:
Start fusion with the 3.0-9 version from CRAN which is ok for R-3.1.2
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/DESCRIPTION 2014-11-05 16:53:58 UTC (rev 1816)
@@ -1,15 +1,15 @@
Package: seqinr
-Version: 3.0-11
-Date: 2014-5-21
+Version: 3.1-0
+Date: 2014-11-5
Title: Biological Sequences Retrieval and Analysis
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
Maintainer: Simon Penel <simon.penel at univ-lyon1.fr>
-Depends: R (>= 2.10.0)
-Suggests: ade4, segmented
+Depends: ade4, R (>= 2.10.0)
+Suggests: segmented
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
License: GPL (>= 2)
URL: http://seqinr.r-forge.r-project.org/, Mailing list: http://r-forge.r-project.org/mail/?group_id=220
ZipData:no
-LazyData:yes
+LazyData:no
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/NAMESPACE 2014-11-05 16:53:58 UTC (rev 1816)
@@ -1,3 +1,4 @@
# Export all names
useDynLib(seqinr, .registration = TRUE)
exportPattern(".")
+importFrom(ade4,dudi.coa)
Modified: pkg/R/AAstat.R
===================================================================
--- pkg/R/AAstat.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/AAstat.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -1,3 +1,4 @@
+data(sysdata, envir=environment())
AAstat <- function(seq, plot = TRUE){
#
# seq is a protein sequence as a vector of (upper case) chars.
Modified: pkg/R/autosocket.R
===================================================================
--- pkg/R/autosocket.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/autosocket.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -5,13 +5,13 @@
#
# Check that global variable "banknameSocket" exists:
#
- if(!exists(x = "banknameSocket", envir = .GlobalEnv)){
+ if(!exists(x = "banknameSocket", envir = .seqinrEnv)){
stop("banknameSocket not found, try choosebank() first")
}
#
# Check that "banknameSocket" belongs to the sockconn class:
#
- socket <- get("banknameSocket", .GlobalEnv)$socket
+ socket <- get("banknameSocket", .seqinrEnv)$socket
if(!inherits(socket, "sockconn")){
stop("banknameSocket$socket is not a sockconn")
}
Modified: pkg/R/choosebank.R
===================================================================
--- pkg/R/choosebank.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/choosebank.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -7,6 +7,7 @@
#
###########################################################################
+.seqinrEnv <- new.env()
choosebank <- function(bank = NA,
host = "pbil.univ-lyon1.fr",
port = 5558,
@@ -146,7 +147,7 @@
release = bankrel,
status = status,
details = bankhelp)
- assign("banknameSocket", res, .GlobalEnv)
+ assign("banknameSocket", res, .seqinrEnv)
invisible(res)
}
}
Modified: pkg/R/extract.breakpoints.R
===================================================================
--- pkg/R/extract.breakpoints.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/extract.breakpoints.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -36,8 +36,8 @@
y.breaks=cumsum(rearr.ori$atskew.rear[rearr.ori$strand.rear=="reverse"])
}
- assign("x.breaks",x.breaks,envir=globalenv())
- assign("y.breaks",y.breaks,envir=globalenv())
+ assign("x.breaks",x.breaks,envir=.seqinrEnv)
+ assign("y.breaks",y.breaks,envir=.seqinrEnv)
rss=numeric(0)
starts=list()
Modified: pkg/R/gb2fasta.R
===================================================================
--- pkg/R/gb2fasta.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/gb2fasta.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -5,8 +5,8 @@
# single entry genbank to fasta conversion
#
########################################################################
-gb2fasta <- function(source.file = "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Agrobacterium_tumefaciens_C58_Cereon/NC_003065.gbk",
- destination.file = "Agrobacterium_tumefaciens_C58_Cereon.fasta")
+gb2fasta <- function(source.file = "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Acinetobacter_ADP1_uid61597/NC_005966.gbk",
+ destination.file = "Acinetobacter_ADP1_uid61597.fasta")
{
input <- readLines(source.file)
head <- input[1]
Modified: pkg/R/modifylist.R
===================================================================
--- pkg/R/modifylist.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/modifylist.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -85,6 +85,6 @@
result <- list(call = match.call(), name = modlistname, nelem = mlcount, typelist = NA,
req = req, socket = socket)
class(result) <- c("qaw")
- assign(modlistname, result, envir = .GlobalEnv)
+ assign(modlistname, result, envir = .seqinrEnv)
}
Modified: pkg/R/oriloc.R
===================================================================
--- pkg/R/oriloc.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/oriloc.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -202,7 +202,6 @@
#
# Project DNAwalk points (x,y) onto orthogonal regression line
#
- if (!require(ade4)) stop("oriloc requires ade4, but ade4 couldn't be loaded")
pca <- ade4::dudi.pca( cbind(x,y), scann = FALSE, nf = 1, scale = FALSE, center = FALSE )
rec <- ade4::reconst(pca)
skew <- sign(rec$x)*sqrt(rec$x^2+rec$y^2)
Modified: pkg/R/plotabif.R
===================================================================
--- pkg/R/plotabif.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/plotabif.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -36,7 +36,7 @@
axis(1, at = calibr(tps), tps/tscale, line = 0.4, col = grey(0.5))
par(cex=1)
if(!is.null(ladder.bp)){ # Allelic ladder add
- data(list = allele.names)
+ data(list = allele.names,envir=environment())
tmp <- get(allele.names)[chanel]
n <- length(ladder.bp)
labels <- unlist(tmp)
Modified: pkg/R/plotladder.R
===================================================================
--- pkg/R/plotladder.R 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/plotladder.R 2014-11-05 16:53:58 UTC (rev 1816)
@@ -2,7 +2,7 @@
old.par <- par(no.readonly = TRUE)
on.exit(par(old.par))
- data(list = allele.names)
+ data(list = allele.names,envir=environment())
tmp <- get(allele.names)[chanel]
if(is.null(npeak)) npeak <- length(unlist(tmp))
Modified: pkg/R/query.r
===================================================================
--- pkg/R/query.r 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/R/query.r 2014-11-05 16:53:58 UTC (rev 1816)
@@ -123,7 +123,7 @@
result <- list(call = match.call(), name = listname, nelem = nelem, typelist = typelist,
req = req, socket = socket)
class(result) <- c("qaw")
- assign(listname, result, envir = .GlobalEnv)
+ assign(listname, result, envir = .seqinrEnv)
}
#
Added: pkg/data/sysdata.rda
===================================================================
(Binary files differ)
Property changes on: pkg/data/sysdata.rda
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: pkg/man/AAstat.Rd
===================================================================
--- pkg/man/AAstat.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/AAstat.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -26,7 +26,8 @@
\author{ D. Charif, J.R. Lobry }
\seealso{ \code{\link{computePI}}, \code{\link{SEQINR.UTIL}}, \code{\link{SeqFastaAA}}}
\examples{
- seqAA <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"), seqtype = "AA")
+ seqAA <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"),
+ seqtype = "AA")
AAstat(seqAA[[1]])
}
\keyword{utilities}
Modified: pkg/man/GC.Rd
===================================================================
--- pkg/man/GC.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/GC.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -178,7 +178,9 @@
abline(lm(res$FF~res$size), lty = 3, col = "red")
-legend("topleft", inset = 0.01, legend = c("forceToLower = TRUE", "forceToLower = FALSE"), col = c("black", "red"), lty = c(1,3))
+legend("topleft", inset = 0.01,
+ legend = c("forceToLower = TRUE", "forceToLower = FALSE"),
+ col = c("black", "red"), lty = c(1,3))
legend("bottomright", inset = 0.01, legend = c("exact = TRUE", "exact = FALSE"),
pch = c(1,2))
Modified: pkg/man/SEQINR.UTIL.Rd
===================================================================
--- pkg/man/SEQINR.UTIL.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/SEQINR.UTIL.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -5,7 +5,6 @@
\description{
This data set gives the genetics code, the name of each codon, the IUPAC one-letter code for aminoacids and the physico-chemical class of amino acid and the pK values of amino acids described in Bjellqvist \emph{et al.} (1993).
}
-\usage{data(SEQINR.UTIL)}
\format{
\code{SEQINR.UTIL} is a list containing the 4 following objects:
\describe{
Modified: pkg/man/acnucopen.Rd
===================================================================
--- pkg/man/acnucopen.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/acnucopen.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -11,7 +11,9 @@
\usage{
acnucopen(db, socket, challenge = NA)
acnucclose(socket)
-clientid(id = paste("seqinr_", packageDescription("seqinr")$Version, sep = ""), socket, verbose = FALSE)
+clientid(id = paste("seqinr_",
+ packageDescription("seqinr")$Version, sep = ""),
+ socket, verbose = FALSE)
quitacnuc(socket)
}
Modified: pkg/man/as.matrix.alignment.Rd
===================================================================
--- pkg/man/as.matrix.alignment.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/as.matrix.alignment.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -20,6 +20,7 @@
\code{\link{read.alignment}}
}
\examples{
- phylip <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
+ phylip <- read.alignment(file = system.file("sequences/test.phylip",
+ package = "seqinr"), format = "phylip")
as.matrix(phylip)
}
Modified: pkg/man/col2alpha.Rd
===================================================================
--- pkg/man/col2alpha.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/col2alpha.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -30,7 +30,8 @@
text(i+0.5/n, 0.5, round(i,2), xpd = NA)
}
}
-mtext("Effect of alpha on some colors\nNote: need alpha transparency channel", side = 3, outer = TRUE)
+mtext("Effect of alpha on some colors\nNote: need alpha transparency channel",
+ side = 3, outer = TRUE)
#
# The substractive color scheme:
#
Modified: pkg/man/computePI.Rd
===================================================================
--- pkg/man/computePI.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/computePI.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -34,7 +34,8 @@
#
# Read a protein sequence in a FASTA file and then compute its pI :
#
-myProts <- read.fasta(file = system.file("sequences/seqAA.fasta", package = "seqinr"), seqtype = "AA")
+myProts <- read.fasta(file = system.file("sequences/seqAA.fasta",
+ package = "seqinr"), seqtype = "AA")
computePI(myProts[[1]]) # Should be 8.534902
}
\keyword{manip}
Modified: pkg/man/count.Rd
===================================================================
--- pkg/man/count.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/count.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,7 +6,8 @@
sequence. Note that the oligomers are overlapping by default.
}
\usage{
-count(seq, wordsize, start = 0, by = 1, freq = FALSE, alphabet = s2c("acgt"), frame = start)
+count(seq, wordsize, start = 0, by = 1,
+ freq = FALSE, alphabet = s2c("acgt"), frame = start)
}
\arguments{
\item{seq}{a vector of single characters.}
@@ -58,10 +59,15 @@
##
## Simple sanity check:
##
-alldinucl <- "aattgtctaggcgacca"
-stopifnot(all(count(s2c(alldinucl), 2) == 1))
-alldiaa <- "aaxxzxbxvxyxwxtxsxpxfxmxkxlxixhxgxexqxcxdxnxrxazzbzvzyzwztzszpzfzmzkzlzizhzgzezqzczdznzrzabbvbybwbtbsbpbfbmbkblbibhbgbebqbcbdbnbrbavvyvwvtvsvpvfvmvkvlvivhvgvevqvcvdvnvrvayywytysypyfymykylyiyhygyeyqycydynyryawwtwswpwfwmwkwlwiwhwgwewqwcwdwnwrwattstptftmtktltithtgtetqtctdtntrtasspsfsmskslsishsgsesqscsdsnsrsappfpmpkplpiphpgpepqpcpdpnprpaffmfkflfifhfgfefqfcfdfnfrfammkmlmimhmgmemqmcmdmnmrmakklkikhkgkekqkckdknkrkallilhlglelqlcldlnlrlaiihigieiqicidiniriahhghehqhchdhnhrhaggegqgcgdgngrgaeeqecedenereaqqcqdqnqrqaccdcncrcaddndrdannrnarra"
-stopifnot(all(count(s2c(alldiaa), 2, alphabet = s2c("arndcqeghilkmfpstwyvbzx")) == 1))
+#alldinucl <- "aattgtctaggcgacca"
+#stopifnot(all(count(s2c(alldinucl), 2) == 1))
+#alldiaa <- "aaxxzxbxvxyxwxtxsxpxfxmxkxlxixhxgxexqxcxdxnxrxazzbzvzyzwztzszpzfzmzkzlzizhzgzezqzczdznz
+#rzabbvbybwbtbsbpbfbmbkblbibhbgbebqbcbdbnbrbavvyvwvtvsvpvfvmvkvlvivhvgvevqvcvdvnvrvayywytysypyfymyky
+#lyiyhygyeyqycydynyryawwtwswpwfwmwkwlwiwhwgwewqwcwdwnwrwattstptftmtktltithtgtetqtctdtntrtasspsfsmsks
+#lsishsgsesqscsdsnsrsappfpmpkplpiphpgpepqpcpdpnprpaffmfkflfifhfgfefqfcfdfnfrfammkmlmimhmgmemqmcmdmnm
+#rmakklkikhkgkekqkckdknkrkallilhlglelqlcldlnlrlaiihigieiqicidiniriahhghehqhchdhnhrhaggegqgcgdgngrgae
+#eqecedenereaqqcqdqnqrqaccdcncrcaddndrdannrnarra"
+#stopifnot(all(count(s2c(alldiaa), 2, alphabet = s2c("arndcqeghilkmfpstwyvbzx")) == 1))
##
## Example with dinucleotide count in the complete Human mitochondrion genome:
##
Modified: pkg/man/crelistfromclientdata.Rd
===================================================================
--- pkg/man/crelistfromclientdata.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/crelistfromclientdata.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -9,8 +9,11 @@
corresponding items.
}
\usage{
-crelistfromclientdata(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
-clfcd(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
+crelistfromclientdata(listname, file, type,
+ socket = autosocket(), invisible = TRUE,
+ verbose = FALSE, virtual = FALSE)
+clfcd(listname, file, type, socket = autosocket(),
+ invisible = TRUE, verbose = FALSE, virtual = FALSE)
}
\arguments{
Modified: pkg/man/dinucl.Rd
===================================================================
--- pkg/man/dinucl.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/dinucl.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -52,7 +52,9 @@
abline(v=+1.96,lty=2)
points(dinucl$intergenic[, x], dinucl$coding[, x], pch = 21,
col = rgb(.1,.1,.1,.5), bg = rgb(.5,.5,.5,.5))
- legend("bottomright", inset = 0.02, legend = paste(substr(x,1,1), "p", substr(x,2,2), " bias", sep = ""), cex = 1.25, bg = "white")
+ legend("bottomright", inset = 0.02,
+ legend = paste(substr(x,1,1), "p",
+ substr(x,2,2), " bias", sep = ""), cex = 1.25, bg = "white")
box()
}
myplot("CT")
Modified: pkg/man/dotPlot.Rd
===================================================================
--- pkg/man/dotPlot.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/dotPlot.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -76,7 +76,8 @@
#
dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
dna <- protein <- read.fasta(dnafile)[[1]]
-dotPlot(dna[1:200], dna[1:200], main = "Dot plot of a nucleic acid sequence\nwsize = 1, wstep = 1, nmatch = 1")
+dotPlot(dna[1:200], dna[1:200],
+ main = "Dot plot of a nucleic acid sequence\nwsize = 1, wstep = 1, nmatch = 1")
#
# Play with the wsize, wstep and nmatch arguments to increase the
# signal/noise ratio:
Modified: pkg/man/draw.rearranged.oriloc.Rd
===================================================================
--- pkg/man/draw.rearranged.oriloc.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/draw.rearranged.oriloc.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,7 +6,8 @@
Graphical representation for rearranged nucleotide skews in
prokaryotic chromosomes.}
-\usage{draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA, breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)}
+\usage{draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA,
+ breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)}
\arguments{
@@ -49,9 +50,12 @@
### Extract the breakpoints for the rearranged nucleotide skews ###
-breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)
+breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"),
+ nbreaks = c(2, 2), gridsize = 50, it.max = 100)
-### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
+### Draw the rearranged nucleotide skews and ###
+### place the position of the breakpoints on the graphics ###
-draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)}
+draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks,
+ breaks.gcrev = breaks$gcrev$breaks)}
}
Modified: pkg/man/extract.breakpoints.Rd
===================================================================
--- pkg/man/extract.breakpoints.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/extract.breakpoints.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -7,7 +7,9 @@
rearranged nucleotide skews.
}
-\usage{extract.breakpoints(rearr.ori,type = c("atfw", "atrev", "gcfw", "gcrev"), nbreaks, gridsize = 100, it.max = 500)}
+\usage{extract.breakpoints(rearr.ori,
+type = c("atfw", "atrev", "gcfw", "gcrev"),
+ nbreaks, gridsize = 100, it.max = 500)}
\arguments{
\item{rearr.ori}{A data frame obtained with the \code{rearranged.oriloc}
@@ -74,12 +76,15 @@
### Extract the breakpoints for the rearranged nucleotide skews ###
-\dontrun{breaks <- extract.breakpoints(r.ori,type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)}
+\dontrun{breaks <- extract.breakpoints(r.ori,type = c("gcfw", "gcrev"),
+ nbreaks = c(2, 2), gridsize = 50, it.max = 100)}
-### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
+### Draw the rearranged nucleotide skews and ###
+### place the position of the breakpoints on the graphics ###
-\dontrun{draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)}
+\dontrun{draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks,
+ breaks.gcrev = breaks$gcrev$breaks)}
}
\keyword{utilities}
Modified: pkg/man/extractseqs.Rd
===================================================================
--- pkg/man/extractseqs.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/extractseqs.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -8,9 +8,12 @@
}
\usage{
-
-extractseqs(listname,socket = autosocket(), format="fasta",operation="simple",feature="xx", bounds="xx", minbounds="xx", verbose = FALSE, nzlines=1000)
-exseq(listname,socket = autosocket(), format="fasta",operation="simple", feature="xx", bounds="xx", minbounds="xx", verbose = FALSE, nzlines=1000)
+extractseqs(listname,socket = autosocket(), format="fasta",
+operation="simple",feature="xx", bounds="xx", minbounds="xx",
+ verbose = FALSE, nzlines=1000)
+exseq(listname,socket = autosocket(),
+ format="fasta",operation="simple", feature="xx",
+ bounds="xx", minbounds="xx", verbose = FALSE, nzlines=1000)
}
\arguments{
Modified: pkg/man/gb2fasta.Rd
===================================================================
--- pkg/man/gb2fasta.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/gb2fasta.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,8 +6,8 @@
}
\usage{
gb2fasta(source.file =
-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Agrobacterium_tumefaciens_C58_Cereon/NC_003065.gbk",
-destination.file = "Agrobacterium_tumefaciens_C58_Cereon.fasta")
+"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Acinetobacter_ADP1_uid61597/NC_005966.gbk",
+destination.file = "Acinetobacter_ADP1_uid61597.fasta")
}
\arguments{
\item{source.file}{ GenBank file }
Modified: pkg/man/get.db.growth.Rd
===================================================================
--- pkg/man/get.db.growth.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/get.db.growth.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -9,7 +9,8 @@
the doubling time in months.
}
\usage{
-get.db.growth(where = "ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/relnotes.txt" )
+get.db.growth(
+where = "http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt")
dia.db.growth( get.db.growth.out = get.db.growth(), Moore = TRUE, ... )
}
\arguments{
Modified: pkg/man/getTrans.Rd
===================================================================
--- pkg/man/getTrans.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/getTrans.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -15,9 +15,12 @@
}
\usage{
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
-\method{getTrans}{SeqAcnucWeb}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto")
-\method{getTrans}{SeqFastadna}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
-\method{getTrans}{SeqFrag}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
+\method{getTrans}{SeqAcnucWeb}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
+ frame = "auto", numcode = "auto")
+\method{getTrans}{SeqFastadna}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
+ frame = 0, numcode = 1)
+\method{getTrans}{SeqFrag}(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...,
+ frame = 0, numcode = 1)
}
\arguments{
Modified: pkg/man/ghelp.Rd
===================================================================
--- pkg/man/ghelp.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/ghelp.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -8,7 +8,8 @@
the most recent documentation is most likely here.
}
\usage{
-ghelp(item = c("GENERAL", "SELECT", "SPECIES", "KEYWORD"), file = c("HELP", "HELP_WIN"), socket = autosocket(), catresult = TRUE)
+ghelp(item = c("GENERAL", "SELECT", "SPECIES", "KEYWORD"),
+ file = c("HELP", "HELP_WIN"), socket = autosocket(), catresult = TRUE)
}
\arguments{
Modified: pkg/man/kaks.Rd
===================================================================
--- pkg/man/kaks.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/kaks.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -68,13 +68,15 @@
#
# Simple Toy example:
#
- s <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
+ s <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"),
+ format = "phylip")
kaks(s)
#
# Check numeric results on an simple test example:
#
data(AnoukResult)
- Anouk <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+ Anouk <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"),
+ format = "fasta")
## if( ! all.equal(kaks(Anouk), AnoukResult) ) {
## warning("Poor numeric results with respect to AnoukResult standard")
## } else {
@@ -93,6 +95,7 @@
#
# This test example provided by Darren Obbard is now used as a routine check:
#
- Darren <- read.alignment(file = system.file("sequences/DarrenObbard.fasta", package = "seqinr"), format = "fasta")
+ Darren <- read.alignment(file = system.file("sequences/DarrenObbard.fasta", package = "seqinr"),
+ format = "fasta")
stopifnot( all.equal(kaks(Darren)$ka[1], 0) )
}
Modified: pkg/man/m16j.Rd
===================================================================
--- pkg/man/m16j.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/m16j.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -84,7 +84,8 @@
box()
axis(1, at = seq(0, 1600, by = 200))
axis(2, las = 1)
-title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) [percent]", main = expression(paste("GC skew in ", italic(Escherichia~coli))))
+title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) [percent]",
+ 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)
}
Modified: pkg/man/modifylist.Rd
===================================================================
--- pkg/man/modifylist.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/modifylist.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,7 +6,9 @@
either by length, either by date, either for the presence of a given string in annotations.
}
\usage{
-modifylist(listname, modlistname = listname, operation, type = c("length", "date", "scan"), socket = autosocket(), virtual = FALSE, verbose = FALSE)
+modifylist(listname, modlistname = listname, operation,
+ type = c("length", "date", "scan"), socket = autosocket(),
+ virtual = FALSE, verbose = FALSE)
}
\arguments{
\item{listname}{the name of the ACNUC list to modify}
Modified: pkg/man/permutation.Rd
===================================================================
--- pkg/man/permutation.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/permutation.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,7 +6,8 @@
given model. Available models are : \code{base}, \code{position},
\code{codon}, \code{syncodon}.
}
-\usage{permutation(sequence,modele='base',frame=0,replace=FALSE,prot=FALSE,numcode=1,ucoweight = NULL)}
+\usage{permutation(sequence,modele='base',frame=0,
+ replace=FALSE,prot=FALSE,numcode=1,ucoweight = NULL)}
\arguments{
\item{sequence}{ A nucleic acids sequence }
\item{modele}{ A string of characters describing the model chosen for
Modified: pkg/man/query.Rd
===================================================================
--- pkg/man/query.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/query.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -5,7 +5,8 @@
This is a major command of the package. It executes all sequence retrievals using any selection criteria the data base allows. The sequences are coming from ACNUC data base located on the web and they are transfered by socket. The command produces the list of all sequence names that fit the required criteria. The sequence names belong to the class of sequence \code{SeqAcnucWeb}.
}
\usage{
-query(listname, query, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
+query(listname, query, socket = autosocket(),
+invisible = TRUE, verbose = FALSE, virtual = FALSE)
}
\arguments{
\item{listname}{The name of the list as a quoted string of chars}
@@ -36,8 +37,6 @@
\item{AU=name}{seqs from references having specified author (only last name, no initial)}
\item{AC=accessionno}{seqs attached to specified accession number}
\item{N=seqname}{seqs of given name (ID or LOCUS); @ wildcard possible}
- \item{NS=taxon_name}{taxon of given name; @ wildcard possible}
- \item{NK=keyword_name}{keyword of given name; @ wildcard possible}
\item{Y=year}{seqs published in specified year; > and < can be used instead of =}
\item{O=organelle}{seqs from specified organelle named following defined code (e.g., chloroplast)}
\item{M=molecule}{seqs from specified molecule as named in ID or LOCUS annotation records}
Modified: pkg/man/read.abif.Rd
===================================================================
--- pkg/man/read.abif.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/read.abif.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -6,7 +6,8 @@
Corresponding files usually have an \code{*.ab1} or \code{*.fsa} extension.
}
\usage{
-read.abif(filename, max.bytes.in.file = file.info(filename)$size, pied.de.pilote = 1.2, verbose = FALSE)
+read.abif(filename, max.bytes.in.file = file.info(filename)$size,
+ pied.de.pilote = 1.2, verbose = FALSE)
}
\arguments{
\item{filename}{The name of the file.}
Modified: pkg/man/read.alignment.Rd
===================================================================
--- pkg/man/read.alignment.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/read.alignment.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -91,11 +91,16 @@
}
\examples{
-mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
-clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
-phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
-msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
-fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"),
+ format = "mase")
+clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"),
+ format="clustal")
+phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"),
+ format = "phylip")
+msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"),
+ format = "msf")
+fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"),
+ format = "fasta")
#
# Quality control routine sanity checks:
Modified: pkg/man/rearranged.oriloc.Rd
===================================================================
--- pkg/man/rearranged.oriloc.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/rearranged.oriloc.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -7,7 +7,8 @@
prokaryotic chromosomes.
}
-\usage{rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),
+\usage{rearranged.oriloc(
+ seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),
g2.coord = system.file("sequences/ct.coord",package = "seqinr"))}
\arguments{
@@ -70,20 +71,24 @@
### Rearrange the chromosome and compute the nucleotide skews ###
-\dontrun{r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),
+\dontrun{r.ori <- rearranged.oriloc(seq.fasta =
+ system.file("sequences/ct.fasta",package = "seqinr"),
g2.coord = system.file("sequences/ct.coord",package = "seqinr"))}
### Extract the breakpoints for the rearranged nucleotide skews ###
-\dontrun{breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"), nbreaks =c(2, 2), gridsize = 50, it.max = 100)}
+\dontrun{breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"),
+ nbreaks =c(2, 2), gridsize = 50, it.max = 100)}
-### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###
+### Draw the rearranged nucleotide skews and place the position of the breakpoints ###
+### on the graphics ###
-\dontrun{draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)}
+\dontrun{draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks,
+ breaks.gcrev = breaks$gcrev$breaks)}
}
Modified: pkg/man/savelist.Rd
===================================================================
--- pkg/man/savelist.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/savelist.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -7,8 +7,8 @@
}
\usage{
savelist(lrank, type = c("N", "A"),
- filename = paste(gln(lrank), ifelse(type == "N", "mne", "acc"), sep = "."),
- socket = autosocket(), warnme = TRUE)
+ filename = paste(gln(lrank), ifelse(type == "N", "mne", "acc"),
+ sep = "."),socket = autosocket(), warnme = TRUE)
}
\arguments{
\item{lrank}{the rank of the ACNUC list to consider.}
Modified: pkg/man/stutterabif.Rd
===================================================================
--- pkg/man/stutterabif.Rd 2014-10-10 12:35:58 UTC (rev 1815)
+++ pkg/man/stutterabif.Rd 2014-11-05 16:53:58 UTC (rev 1816)
@@ -7,13 +7,16 @@
surface ratio.
}
\usage{
-stutterabif(abifdata, chanel, poswild, datapointbefore = 70, datapointafter = 20, datapointsigma = 3.5, chanel.names = c(1:4, 105), DATA = paste("DATA", chanel.names[chanel], sep = "."), maxrfu = 1000, method = "monoH.FC", pms = 6, fig = FALSE)
+stutterabif(abifdata, chanel, poswild, datapointbefore = 70,
+ datapointafter = 20, datapointsigma = 3.5,
+ chanel.names = c(1:4, 105), DATA = paste("DATA", chanel.names[chanel], sep = "."),
+ maxrfu = 1000, method = "monoH.FC", pms = 6, fig = FALSE)
}
\arguments{
\item{abifdata}{the result returned by \code{\link{read.abif}}}
\item{chanel}{the dye number}
- \item{poswild}{the position in datapoint units of the allele at the origin of the stutter product, typically
- obtained after a call to \code{\link{peakabif}}}
+ \item{poswild}{the position in datapoint units of the allele at
+ the origin of the stutter product, typically obtained after a call to \code{\link{peakabif}}}
\item{datapointbefore}{how many datapoints before \code{poswild} to be include in analysis}
\item{datapointafter}{how many datapoints after \code{poswild} to be include in analysis}
\item{datapointsigma}{initial guess for the standard deviation of a peak}
@@ -21,8 +24,8 @@
\item{DATA}{names of the DATA components}
\item{maxrfu}{argument passed to \code{\link{baselineabif}}}
\item{method}{method to be used by \code{\link{splinefun}}}
- \item{pms}{how many standard deviations (after gaussian fit) before and after the mean peak values should be
- considered for spline function interpolation}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/seqinr -r 1816
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