[adegenet-commits] r1053 - pkg pkg/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 20 13:00:42 CET 2012
Author: jombart
Date: 2012-11-20 13:00:42 +0100 (Tue, 20 Nov 2012)
New Revision: 1053
Modified:
pkg/DESCRIPTION
pkg/R/sequences.R
www/literature.html
Log:
+1 ref
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-11-15 15:50:59 UTC (rev 1052)
+++ pkg/DESCRIPTION 2012-11-20 12:00:42 UTC (rev 1053)
@@ -10,6 +10,6 @@
Suggests: genetics, spdep, tripack, pegas, seqinr, adehabitat, multicore, akima, maps, splancs, hierfstat
Depends: R (>= 2.10), methods, MASS, ade4, igraph, ape
Description: Classes and functions for genetic data analysis within the multivariate framework.
-Collate: classes.R basicMethods.R handling.R auxil.R setAs.R SNPbin.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R simOutbreak.R zzz.R
+Collate: classes.R basicMethods.R handling.R auxil.R setAs.R SNPbin.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R simOutbreak.R mutations.R zzz.R
License: GPL (>=2)
LazyLoad: yes
Modified: pkg/R/sequences.R
===================================================================
--- pkg/R/sequences.R 2012-11-15 15:50:59 UTC (rev 1052)
+++ pkg/R/sequences.R 2012-11-20 12:00:42 UTC (rev 1053)
@@ -155,59 +155,59 @@
-#################
-## findMutations
-#################
+## #################
+## ## findMutations
+## #################
-## GENERIC
-findMutations <- function(...){
- UseMethod("findMutations")
-}
+## ## GENERIC
+## findMutations <- function(...){
+## UseMethod("findMutations")
+## }
-## METHOD FOR DNABIN
-findMutations.DNAbin <- function(x, from=NULL, to=NULL, ...){
- ## CHECKS ##
- if(!require(ape)) stop("the ape package is needed")
- if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
- x <- as.matrix(x)
+## ## METHOD FOR DNABIN
+## findMutations.DNAbin <- function(x, from=NULL, to=NULL, ...){
+## ## CHECKS ##
+## if(!require(ape)) stop("the ape package is needed")
+## if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+## x <- as.matrix(x)
- ## function to pull out mutations from sequence a to b ##
- NUCL <- c('a','t','g','c')
- f1 <- function(a,b){
- seqa <- as.character(x[a,])
- seqb <- as.character(x[b,])
- temp <- which(seqa != seqb)
- ori <- seqa[temp]
- mut <- seqb[temp]
- names(ori) <- names(mut) <- temp
- toRemove <- !ori %in% NUCL | !mut %in% NUCL
- ori <- ori[!toRemove]
- mut <- mut[!toRemove]
- if(all(toRemove)) return(NULL)
- res <- data.frame(ori,mut)
- names(res) <- rownames(x)[c(a,b)]
- res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
- return(res)
- }
+## ## function to pull out mutations from sequence a to b ##
+## NUCL <- c('a','t','g','c')
+## f1 <- function(a,b){
+## seqa <- as.character(x[a,])
+## seqb <- as.character(x[b,])
+## temp <- which(seqa != seqb)
+## ori <- seqa[temp]
+## mut <- seqb[temp]
+## names(ori) <- names(mut) <- temp
+## toRemove <- !ori %in% NUCL | !mut %in% NUCL
+## ori <- ori[!toRemove]
+## mut <- mut[!toRemove]
+## if(all(toRemove)) return(NULL)
+## res <- data.frame(ori,mut)
+## names(res) <- rownames(x)[c(a,b)]
+## res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
+## return(res)
+## }
- ## GET LIST OF PAIRS TO COMPARE ##
- ## handle NULL
- if(is.null(from)) from <- 1:nrow(x)
- if(is.null(to)) to <- 1:nrow(x)
+## ## GET LIST OF PAIRS TO COMPARE ##
+## ## handle NULL
+## if(is.null(from)) from <- 1:nrow(x)
+## if(is.null(to)) to <- 1:nrow(x)
- ## get pairs
- pairs <- expand.grid(from, to)
+## ## get pairs
+## pairs <- expand.grid(from, to)
- ## remove unwanted comparisons
- pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
+## ## remove unwanted comparisons
+## pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
- ## GET NUMBER OF MUTATIONS ##
- out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
- names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
+## ## GET NUMBER OF MUTATIONS ##
+## out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
+## names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
- return(out)
+## return(out)
-} # end findMutations
+## } # end findMutations
@@ -215,39 +215,39 @@
-##################
-## graphMutations
-##################
+## ##################
+## ## graphMutations
+## ##################
-## GENERIC
-graphMutations <- function(...){
- UseMethod("graphMutations")
-}
+## ## GENERIC
+## graphMutations <- function(...){
+## UseMethod("graphMutations")
+## }
-## METHOD FOR DNABIN
-graphMutations.DNAbin <- function(x, from=NULL, to=NULL, plot=TRUE, edge.curved=TRUE, ...){
- if(!require(igraph)) stop("igraph is required")
+## ## METHOD FOR DNABIN
+## graphMutations.DNAbin <- function(x, from=NULL, to=NULL, plot=TRUE, edge.curved=TRUE, ...){
+## if(!require(igraph)) stop("igraph is required")
- ## GET MUTATIONS ##
- x <- findMutations(x, from=from, to=to)
+## ## GET MUTATIONS ##
+## x <- findMutations(x, from=from, to=to)
- ## GET GRAPH ##
- from <- gsub("->.*","",names(x))
- to <- gsub(".*->","",names(x))
- vnames <- sort(unique(c(from,to)))
- dat <- data.frame(from,to,stringsAsFactors=FALSE)
- out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
+## ## GET GRAPH ##
+## from <- gsub("->.*","",names(x))
+## to <- gsub(".*->","",names(x))
+## vnames <- sort(unique(c(from,to)))
+## dat <- data.frame(from,to,stringsAsFactors=FALSE)
+## out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
- ## SET ANNOTATIONS FOR THE BRANCHES ##
- annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
- E(out)$label <- annot
- E(out)$curved <- edge.curved
+## ## SET ANNOTATIONS FOR THE BRANCHES ##
+## annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
+## E(out)$label <- annot
+## E(out)$curved <- edge.curved
- ## PLOT / RETURN ##
- if(plot) plot(out, ...)
+## ## PLOT / RETURN ##
+## if(plot) plot(out, ...)
- return(out)
-} # end graphMutations
+## return(out)
+## } # end graphMutations
Modified: www/literature.html
===================================================================
--- www/literature.html 2012-11-15 15:50:59 UTC (rev 1052)
+++ www/literature.html 2012-11-20 12:00:42 UTC (rev 1053)
@@ -1,10 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
- <head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
- <title>documentation</title>
- <script type="text/javascript">
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>documentation</title>
+ <script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -17,1337 +17,961 @@
})();
</script>
- <meta http-equiv="content-type" content="text/html;
- charset=ISO-8859-1">
- </head>
- <body>
- <br>
- <br>
- <br>
- <div style="margin-left: 40px;"><span style="text-decoration:
- underline;">To cite adegenet:</span><br>
- <br>
- <span style="color: rgb(0, 153, 0);">Jombart T</span><span
- style="color: rgb(0, 153, 0);">.</span><span style="color:
- rgb(0, 153, 0);"> (</span><span style="font-style: italic;
- color: rgb(0, 153, 0);"></span><span style="color: rgb(0, 153,
- 0);">2008)</span><span style="font-weight: bold; color: rgb(0,
- 153, 0);"> </span><span style="color: rgb(0, 153, 0);">adegenet:
- a R package for the
- multivariate analysis of genetic markers. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);"> </span><span
- style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
- style="color: rgb(0, 153, 0);">: 1403-1405. doi:
- 10.1093/bioinformatics/btn129 [</span><a style="color: rgb(0,
- 153, 0);"
-href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a><span
- style="color: rgb(0, 153, 0);"> to a free pdf]</span><br>
- <br>
- <span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I.
- (2011) </span><span style="font-style: italic; color: rgb(0,
- 153, 0);">adegenet 1.3-1</span><span style="color: rgb(0, 153,
- 0);">: new tools for the analysis of
- genome-wide SNP data. </span><span style="font-style: italic;
- color: rgb(0, 153, 0);">Bioinformatics</span><span style="color:
- rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
- style="color: rgb(0, 153, 0);"
-href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
- to
- the
- bublisher's
- website</a><span style="color: rgb(0, 153, 0);">]</span> <br
- style="color: rgb(0, 153, 0);">
- <br>
- <br style="color: rgb(0, 153, 0);">
- <br>
- <span style="text-decoration: underline;">Related publications:<br>
- <br style="text-decoration: underline;">
- </span>- a review of applications of multivariate analyses to
- genetic
- markers data:<br>
- <b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
- style="font-style: italic;"></span> Genetic markers in the
- playground
- of multivariate analysis. <span style="font-style: italic;">Heredity
- </span><span style="font-weight: bold;">102</span>: 330-341.
- doi:10.1038/hdy.2008.130<span style="font-style: italic;">. </span>[<a
-href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy2008130a.pdf">link</a>
- to the journal's pdf - <a target="_new"
-href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free
- abstract</a>]<br>
- <br>
- - the paper presenting the <span style="font-style: italic;">spatial
-principal
- component analysis</span> (<span style="font-style: italic;">sPCA</span>,
- function
- <span style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
- global
- and
- local
- tests
- (<span style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
- and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
- <b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b>
- </b>Revealing
- cryptic
- spatial
- patterns
- in
- genetic variability by a new multivariate
- method. <span style="font-style: italic;">Heredity</span> <span
- style="font-weight: bold;">101</span>: 92-103. doi:
- 10.1038/hdy.2008.34 [<a
-href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
- on the journal's website - <a target="_new"
-href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free
- abstract</a>]<br>
- </div>
- <br>
- <div style="margin-left: 40px;"><span style="font-family: monospace;
- font-weight: bold;"></span><span style="font-family: monospace;
- font-weight: bold;"></span>- the paper
- presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
- (<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
- and
- simulations
- of
- genealoies
- of
- haplotypes
- (<span style="font-family: monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
- <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
- Reconstructing
- disease outbreaks from genetic data: a graph approach. <span
- style="font-style: italic;">Heredity</span>. Doi:
- 10.1038/hdy.2010.78<br>
- <br>
- - the paper introducing the <span style="font-style: italic;">Discriminant
- Analysis
- of
- Principal
- Components</span> (<span style="font-style: italic;">DAPC</span>,
- functions <span style="font-family: monospace;"><span
- style="color: rgb(255, 0, 0);">find.clusters</span> </span>and
- <span style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<br>
- <b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
- Discriminant analysis of principal components: a new method for
- the
- analysis of genetically structured populations. <i>BMC Genetics</i>
- <strong>11</strong><strong>:</strong>94.
- <span>doi:10.1186/1471-2156-11-94</span> [<a
- href="files/DAPCpaper.pdf">free
- pdf</a>] [<a href="http://www.biomedcentral.com/1471-2156/11/94">free
-html
- version</a>] [<a href="reviewDAPC.html">evaluation by Laurent
- Excoffier on F1000</a>] <br>
- <br>
- <br>
- <br>
- <span style="text-decoration: underline;">Publications citing
- adegenet:</span><br style="text-decoration: underline;">
- <br>
- [1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan
- M,
- Kempenaers B, Allainé D (2007) The<span style="color:
- rgb(0, 0, 0);"> genetic similarity between pair members
- influences the frequency of extrapair paternity in alpine
- marmots</span>.
- <i>Animal Behaviour</i><i> </i><span style="font-weight: bold;">76</span>:
- 87-95.<br>
- <br>
- [2] Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi
- VS,
- Smith DG (2008) Pyrosequencing as a method for SNP identification
- in
- the rhesus macaque (<em>Macaca mulatta</em>). <span
- class="citation-abbreviation"><span style="font-style: italic;">BMC
- Genomics</span></span><span class="citation-publication-date">
- </span><span style="font-weight: bold;" class="citation-volume">9</span><span
- class="citation-issue"></span>: 256.<br>
- <div><span class="citation-flpages"><br>
- [3] </span>Kanthaswamy S, Satkoski J, George D, Kou A,
- Erickson BJ,
- Smith DG. (2008). Interspecies hybridization and the
- stratification of
- nuclear genetic variation of rhesus (<span style="font-style:
- italic;">Macaca
- mulatta</span>) and long-tailed macaques (<span
- style="font-style: italic;">Macaca </span><span
- style="font-style: italic;">fascicularis</span>). <span
- style="font-style: italic;">Int J Primatol</span> <span
- style="font-weight: bold;">29</span>: 1295-1311.<br>
- <br>
- [4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde
- AI
- (2009). Hybridization between escaped domestic and wild American
- mink (<span style="font-style: italic;">Neovison vison</span>).
- <span style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1175-1186.<br>
- <br>
- [5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009).
- Age-specific effect of heterozygosity on survival in alpine
- marmots, <span class="i"><span style="font-style: italic;">Marmota
- marmota</span>.</span><span style="font-style: italic;">
- Molecular Ecology</span> <span style="font-weight: bold;">18</span>:
- 1491-1503.<br>
- <br>
- [6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F,
- Ruette
- S, Pontier D (2009). Preserving genetic integrity in a
- hybridising
- world:<br>
- are European Wildcats (<span style="font-style: italic;">Felis
- silvestris silvestris</span>) in eastern France distinct from
- sympatric
- feral domestic cats? <span style="font-style: italic;">Biodivers
- Conserv</span> <span style="font-weight: bold;">18</span>:
- 2351-2360.<br>
- <br>
- [7] Kanthaswamy S <span style="font-style: italic;">et al.</span>
- (2009). Canine Population Data Generated from a Multiplex STR
- Kit for
- Use in Forensic Casework. <span style="font-style: italic;">Journal
- of
- Forensic Sciences</span> <span style="font-weight: bold;">54</span>:
- 829-840.<br>
- <br>
- [8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009).
- Evolutionary
- limits ameliorate the negative impact of an invasive plant. <span
- style="font-style: italic;">Proceedings of the National
- Academy of
- Sciences</span> <span style="font-weight: bold;">106</span>:
- 15362-15367.<br>
- <br>
- [9] Dutech C, Fabreguettes O, Capdevielle X, Robin C (2009)
- Multiple
- introductions of divergent genetic lineages in an invasive
- fungal
- pathogen, Cryphonectria parasitica, in France. <span
- style="font-style: italic;">Heredity</span> (advanced online)
- doi:
- 10.1038/hdy.2009.164.<br>
- <br>
- [10] L Y Rutledge, C J Garroway, K M Loveless and
- B
- R Patterson (2010) Genetic differentiation of eastern
- wolves in
- Algonquin Park despite bridging gene flow between coyotes and
- grey
- wolves.<span style="font-style: italic;"> Heredity</span>
- (advanced
- online) doi: 10.1038/hdy.2010.6.<br>
- <br>
- [11] Jennifer Paul, Nicole Vachon,
- Colin J. Garroway and Joanna R. Freeland
- (2010)
- Molecular data provide strong evidence of natural hybridization
- between
- native and introduced lineages of <i>Phragmites australis</i>
- in North
- America. <span style="font-style: italic;">Biological Invasions</span>.
- doi:
- 10.1007/s10530-010-9699-6.<br>
- <br>
- [12] C. BERTHOULY, D. DO NGOC, S. THÉVENON, D. BOUCHEL,
- T. NHU
- VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI, J.-C.
- MAILLARD
- (2009) How does farmer connectivity influence livestock genetic
- structure? A case-study in a Vietnamese goat population. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 3980-3991<br>
- <br>
- [13] <span class="name"><span class="forenames">COLIN J.</span>
- <span class="surname">GARROWAY</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">JEFF</span> <span
- class="surname">BOWMAN</span></span>,
- <span class="name"><span class="forenames">TARA J.</span> <span
- class="surname">CASCADEN</span></span>, <span class="name"><span
- class="forenames">GILLIAN L.</span> <span class="surname">HOLLOWAY</span></span>,
- <span class="name"><span class="forenames">CAROLYN G.</span> <span
- class="surname">MAHAN</span></span>, <span class="name"><span
- class="forenames">JAY R.</span> <span class="surname">MALCOLM</span></span>,
- <span class="name"><span class="forenames">MICHAEL A.</span> <span
- class="surname">STEELE</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">GREGORY</span> <span
- class="surname">TURNER</span></span> and <span class="name"><span
- class="forenames">PAUL J.</span> <span class="surname">WILSON</span>
- (2009) </span>Climate change induced hybridization in flying
- squirrels. <span style="font-style: italic;">Global Change
- Biology</span>
- <span style="font-weight: bold;">16</span>: 113-121.<br>
- <br>
- [14] <span class="name"><span class="forenames">JOSSELIN</span>
- <span class="surname">MONTARRY</span></span>, <span
- class="name"><span class="forenames">DIDIER</span> <span
- class="surname">ANDRIVON</span>,</span>
- <span class="name"><span class="forenames">ISABELLE</span> <span
- class="surname">GLAIS</span></span>, <span class="name"><span
- class="forenames">ROSELYNE</span> <span class="surname">CORBIERE</span></span>,
- <span class="name"><span class="forenames">GLADYS</span> <span
- class="surname">MIALDEA</span></span> and <span
- class="name"><span class="forenames">FRANCOIS</span> <span
- class="surname">DELMOTTE
- (2010)</span></span> Microsatellite markers reveal two
- admixed genetic
- groups and an ongoing displacement within the French population
- of the
- invasive plant pathogen <span class="i"><span
- style="font-style: italic;">Phytophthora infestans</span>. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">19</span>: <span
- style="text-decoration: underline;"></span></span>1965-1977<br>
- <br>
- [15] Gwenaelle Comont, Marie-France Corio-Costet,
- Philippe Larignon and François Delmotte (2010)
- AFLP
- markers reveal two genetic groups in the French population of
- the
- grapevine fungal pathogen <i>Phaeomoniella chlamydospora.
- European
- Journal of Plant Pathology</i> Doi: 10.1007/s10658-010-9611-3<br>
- <br>
- [16] <span class="name"><span class="forenames">Michelle F.</span>
- <span class="surname">DiLeo</span></span>, <span class="name"><span
- class="forenames">Jeffrey R.</span> <span class="surname">Row</span></span>
- and <span class="name"><span class="forenames">Stephen C.</span>
- <span class="surname">Lougheed (2010)</span></span> Discordant
- patterns of
- population structure for two co-distributed snake species across
- a
- fragmented Ontario landscape. <span style="font-style: italic;">Diversity
- and
- Distributions.</span> Doi: <span class="doi">10.1111/j.1472-4642.2010.00667.x<br>
- <br>
- [17] </span><span class="name"><span class="forenames">Francisco</span>
- <span class="surname">Balao</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">Luis M.</span> <span
- class="surname">Valente</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">Pablo</span> <span
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