[Wavetiling-commits] r41 - in pkg: . pd.atdschip.tiling pd.atdschip.tiling/R pd.atdschip.tiling/data pd.atdschip.tiling/inst pd.atdschip.tiling/inst/UnitTests pd.atdschip.tiling/inst/extdata pd.atdschip.tiling/man waveTiling waveTilingData waveTilingData/data waveTilingData/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 21 14:47:00 CEST 2012
Author: kdbeuf
Date: 2012-05-21 14:46:59 +0200 (Mon, 21 May 2012)
New Revision: 41
Added:
pkg/pd.atdschip.tiling/
pkg/pd.atdschip.tiling/DESCRIPTION
pkg/pd.atdschip.tiling/NAMESPACE
pkg/pd.atdschip.tiling/R/
pkg/pd.atdschip.tiling/R/all.R
pkg/pd.atdschip.tiling/data/
pkg/pd.atdschip.tiling/data/bgSequence.rda
pkg/pd.atdschip.tiling/data/pmSequence.rda
pkg/pd.atdschip.tiling/inst/
pkg/pd.atdschip.tiling/inst/UnitTests/
pkg/pd.atdschip.tiling/inst/UnitTests/Makefile
pkg/pd.atdschip.tiling/inst/UnitTests/checkTables_test.R
pkg/pd.atdschip.tiling/inst/UnitTests/crlmm_test.R
pkg/pd.atdschip.tiling/inst/UnitTests/runall.sh
pkg/pd.atdschip.tiling/inst/UnitTests/runalltests.R
pkg/pd.atdschip.tiling/inst/UnitTests/runfile.sh
pkg/pd.atdschip.tiling/inst/extdata/
pkg/pd.atdschip.tiling/inst/extdata/pd.atdschip.tiling.sqlite
pkg/pd.atdschip.tiling/man/
pkg/pd.atdschip.tiling/man/pkg.Rd
pkg/pd.atdschip.tiling/man/probeSequences.Rd
pkg/waveTiling/
pkg/waveTiling/TODO
pkg/waveTilingData/
pkg/waveTilingData/DESCRIPTION
pkg/waveTilingData/NAMESPACE
pkg/waveTilingData/data/
pkg/waveTilingData/data/leafdev.rda
pkg/waveTilingData/data/leafdevFit.rda
pkg/waveTilingData/data/leafdevInfCompare.rda
pkg/waveTilingData/data/leafdevMapAndFilterTAIR9.rda
pkg/waveTilingData/data/tair9gff.rda
pkg/waveTilingData/external_data_store.txt
pkg/waveTilingData/man/
pkg/waveTilingData/man/leafdev.Rd
pkg/waveTilingData/man/leafdevFit.Rd
pkg/waveTilingData/man/leafdevInfCompare.Rd
pkg/waveTilingData/man/leafdevMapAndFilterTAIR9.Rd
pkg/waveTilingData/man/tair9gff.Rd
Removed:
pkg/CHANGELOG
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/
pkg/TODO
pkg/inst/
pkg/man/
pkg/src/
pkg/vignettes/
Log:
added data and annotation packages
Deleted: pkg/CHANGELOG
===================================================================
--- pkg/CHANGELOG 2012-05-21 09:23:13 UTC (rev 40)
+++ pkg/CHANGELOG 2012-05-21 12:46:59 UTC (rev 41)
@@ -1,3 +0,0 @@
-2011-12-04 Kristof De Beuf <kristof.debeuf at ugent.be> - committed version 0.1.1
-
-* First version
Deleted: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-05-21 09:23:13 UTC (rev 40)
+++ pkg/DESCRIPTION 2012-05-21 12:46:59 UTC (rev 41)
@@ -1,19 +0,0 @@
-Package: waveTiling
-Version: 0.99.0
-Date: 2012-05-14
-License: GPL (>=2)
-Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
-Author: Kristof De Beuf <kristof.debeuf at UGent.be>, Peter Pipelers <peter.pipelers at ugent.be> and Lieven Clement <lieven.clement at gmail.com>
-Maintainer: Kristof De Beuf <kristof.debeuf at UGent.be>
-Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
-Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges
-Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling
-Description: This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.
-Collate: allClasses.R allGenerics.R helperFunctions.R
- initialize-methods.R methods-MapFilterProbe.R
- methods-WaveTilingFeatureSet.R methods-WfmFit.R methods-WfmInf.R show-methods.R
-URL: https://r-forge.r-project.org/projects/wavetiling/
-LazyLoad: yes
-LazyData:
-biocViews: MicroArray, DifferentialExpression, TimeCourse, GeneExpression
-Packaged: 2011-12-05 20:18:51 UTC; kdebeuf
Deleted: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-05-21 09:23:13 UTC (rev 40)
+++ pkg/NAMESPACE 2012-05-21 12:46:59 UTC (rev 41)
@@ -1,74 +0,0 @@
-useDynLib("waveTiling")
-
-## Import Classes
-importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, MIAxE,
- Versions)
-
-importClassesFrom(methods, array, character, data.frame, list, matrix,
- numeric, vector)
-
-importClassesFrom(oligoClasses, TilingFeatureSet)
-
-## Import Methods
-importMethodsFrom(affy, pm, pmindex)
-
-importMethodsFrom(Biobase, exprs, "exprs<-", pData, "phenoData<-")
-
-importMethodsFrom(Biostrings, complement, matchPDict, PDict,
- reverseComplement, startIndex)
-
-importMethodsFrom(GenomicRanges, seqnames)
-
-importMethodsFrom(IRanges, as.matrix, cbind, findOverlaps, ifelse, intersect,
- lapply, mad, Map, mean, median, ncol, nrow, order, paste,
- pintersect, pmin,queryHits, rbind, reduce, Reduce, Rle,
- rownames,"rownames<-", sapply, stack, start, subjectHits,
- subseq, t, table, tapply, unique, unlist, values,
- "values<-", which, width)
-
-importMethodsFrom(methods, initialize, show)
-
-importMethodsFrom(oligo, pmChr, pmPosition, pmSequence, pmStrand)
-
-## Import
-importFrom(affy, bg.adjust, list.celfiles)
-
-importFrom(preprocessCore, normalize.quantiles)
-
-#importFrom(GenomeGraphs, DisplayPars, gdPlot, makeAnnotationTrack,
-# makeGenericArray, makeGenomeAxis, makeRectangleOverlay,
-# makeTextOverlay)
-
-importFrom(GenomicRanges, GRanges, GRangesList)
-
-importFrom(IRanges, IRanges)
-
-importFrom(methods, "@<-", callNextMethod, new)
-
-importFrom(oligo, read.celfiles)
-
-importFrom(stats, contr.helmert, contr.treatment, lm, pnorm, qnorm,
- rnorm)
-
-importFrom(waveslim, wave.filter)
-
-## Export Classes
-#exportClasses(WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf, WfmFitTime, WfmFitFactor, WfmFitCircadian, WfmFitCustom, WfmInfCompare, WfmInfEffects )
-exportClasses(WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf)
-
-## Export Methods
-exportMethods(show)
-
-
-## WaveTilingFeatureSet
-exportMethods(addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet,bgCorrQn,wfm.fit)
-
-## MapFilterProbe
-exportMethods(getFilteredIndices, getPosition, selectProbesFromFilterOverlap)
-
-## WfmFit and WfmInf
-exportMethods(getProbePosition, getNoProbes, getBetaWav, getVarBetaWav, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getDesignMatrix, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj,getPrior, getAlpha, getDelta, getTwoSided, getSigProbes,getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff,getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions, plotWfm)
-
-## Other
-export(cel2TilingFeatureSet, makeContrasts, makeDesign)
-
Deleted: pkg/TODO
===================================================================
--- pkg/TODO 2012-05-21 09:23:13 UTC (rev 40)
+++ pkg/TODO 2012-05-21 12:46:59 UTC (rev 41)
@@ -1,12 +0,0 @@
-
-1) plot function: create argument contrasts to plot specific contrasts
-2) wfm.inference: check calculation of confidence intervals
-3) plot: introduce option to give groupnames to put on Y-axis of plot
-4) getNonAnnotatedRegions: make function more generic wrt how the strands and features in the annotation file are defined
-5) getNonAnnotatedRegions: include option to give max./mean expression / FC per region
-6) getNonAnnotatedRegions: add option to set threshold for minimum density of probes within the regions
-7) getSigGenes: add option to include thresholds (density, outliers,...)
-8) getSigGenes: add option to also detect regions that don't overlap but are in the neighbourhood of annotated regions
-9) getSigGenes: add option to include mean / max expression / FC for each gene
-
-
Added: pkg/pd.atdschip.tiling/DESCRIPTION
===================================================================
--- pkg/pd.atdschip.tiling/DESCRIPTION (rev 0)
+++ pkg/pd.atdschip.tiling/DESCRIPTION 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,18 @@
+Package: pd.atdschip.tiling
+Title: Platform Design Info for Affymetrix Atdschip_tiling
+Description: Platform Design Info for Affymetrix Atdschip_tiling
+Version: 0.0.1
+Author: Kristof De Beuf
+Maintainer: Kristof De Beuf <kristof.debeuf at ugent.be>
+LazyLoad: yes
+Depends: R (>= 2.14.0),
+ methods,
+ RSQLite (>= 0.10.0),
+ oligoClasses (>= 1.15.58),
+ oligo (>= 1.17.3),
+ DBI
+Imports: Biostrings (>= 2.21.11),
+ IRanges (>= 1.11.31)
+License: Artistic-2.0
+biocViews: AnnotationData
+ZipData: no
Added: pkg/pd.atdschip.tiling/NAMESPACE
===================================================================
--- pkg/pd.atdschip.tiling/NAMESPACE (rev 0)
+++ pkg/pd.atdschip.tiling/NAMESPACE 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,7 @@
+import(DBI)
+import(RSQLite)
+export(
+ 'pd.atdschip.tiling'
+ )
+importFrom("Biostrings", "DNAStringSet")
+importFrom("IRanges", "DataFrame")
Added: pkg/pd.atdschip.tiling/R/all.R
===================================================================
--- pkg/pd.atdschip.tiling/R/all.R (rev 0)
+++ pkg/pd.atdschip.tiling/R/all.R 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,53 @@
+globals <- new.env(hash=TRUE, parent=emptyenv())
+
+globals$DEBUG <- FALSE
+
+## setup the path at package level so that DB can be accessed
+## during package install/lazyload db creation.
+##
+## We reset the DB_PATH in .onLoad since we need to
+## get the right one based on libpath
+globals$DB_PATH <- system.file("extdata", "pd.atdschip.tiling.sqlite",
+ package="pd.atdschip.tiling")
+if (nchar(globals$DB_PATH) == 0)
+ stop("Unable to locate DB file")
+
+initDbConnection <- function() {
+ globals$dbCon <- dbConnect(dbDriver("SQLite"), dbname=globals$DB_PATH)
+ globals$dbCon
+}
+
+getDb <- function() {
+ if (!is.null(globals$dbCon) && isIdCurrent(globals$dbCon))
+ return(globals$dbCon)
+ initDbConnection()
+}
+
+closeDb <- function() {
+ ## FIXME: check for valid connection?
+ sapply(dbListResults(globals$dbCon), dbClearResult)
+ dbDisconnect(globals$dbCon)
+ remove(list="dbCon", envir=globals)
+}
+
+.onLoad <- function(libname, pkgname) {
+ require(SQLite, quietly=TRUE)
+ globals$DB_PATH <- system.file("extdata", "pd.atdschip.tiling.sqlite",
+ package="pd.atdschip.tiling",
+ lib.loc=libname)
+ if (nchar(globals$DB_PATH) == 0)
+ stop("Unable to locate DB file")
+ ## Establish a connection to the SQLite DB
+ initDbConnection()
+}
+
+.onUnload <- function(libpath) {
+ closeDb()
+}
+
+pd.atdschip.tiling <- new("AffyTilingPDInfo",
+ genomebuild="TAIR8",
+ getdb=getDb,
+ geometry=as.integer(strsplit("2560;2560", ";")[[1]]),
+ annotation="pd.atdschip.tiling")
+
Added: pkg/pd.atdschip.tiling/data/bgSequence.rda
===================================================================
(Binary files differ)
Property changes on: pkg/pd.atdschip.tiling/data/bgSequence.rda
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/pd.atdschip.tiling/data/pmSequence.rda
===================================================================
(Binary files differ)
Property changes on: pkg/pd.atdschip.tiling/data/pmSequence.rda
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/pd.atdschip.tiling/inst/UnitTests/Makefile
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/Makefile (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/Makefile 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,23 @@
+TOP=../../..
+RUNIT_DIR=$(shell pwd)
+INST_PATH=$(shell dirname ${RUNIT_DIR})
+PKG_PATH=$(shell dirname ${INST_PATH})
+
+ifndef RCMD
+RCMD=R
+endif
+
+all: install test
+
+install:
+ cd ${TOP}; \
+ ${RCMD} CMD INSTALL --clean ${PKG_PATH} && \
+ cd ${RUNIT_DIR}
+
+test:
+ ${RCMD} --slave < runalltests.R
+
+%.R: FORCE
+ ./runfile.sh $@
+
+FORCE:
Added: pkg/pd.atdschip.tiling/inst/UnitTests/checkTables_test.R
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/checkTables_test.R (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/checkTables_test.R 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,86 @@
+pdinfo <- pd.atdschip.tiling
+
+## if SNP 5.0 or 6.0, genomewide == TRUE
+genomewide <- length(grep("CNV", dbListTables(db(pdinfo)))) > 0
+
+test_table_set <- function() {
+ ##
+ ## this test assumes we know what tables have been defined. if we
+ ## change the schema, this test needs to be updated
+ ##
+
+ if (!genomewide){
+ alltabs.sort <- sort(c("featureSet", "mmfeature", "pm_mm", "pmfeature",
+ "qcmmfeature", "qcpm_qcmm", "qcpmfeature",
+ "sequence", "sqlite_stat1", "table_info",
+ "fragmentLength"))
+ }else{
+ alltabs.sort <- sort(c("featureSet", "pmfeature", "sequence",
+ "table_info", "featureSetCNV",
+ "pmfeatureCNV", "sequenceCNV", "sqlite_stat1",
+ "fragmentLength", "fragmentLengthCNV"))
+ }
+
+ dd <- pdinfo at getdb()
+ ll <- sort(dbListTables(dd))
+ checkEquals(alltabs.sort, ll)
+}
+
+test_table_info <- function() {
+ ##
+ ## this test verifies that the table_info table knows the correct
+ ## number of rows for featureSet, and that we can get the featureSet
+ ## table into R to count them for 50K chip this is reasonable --
+ ## actually a little slow but maybe worth it
+ ##
+ ## replacing "select *" by "select fsetid" to speed up
+
+ dd <- pdinfo at getdb()
+ tinfo <- dbGetQuery(dd, "select * from table_info")
+ nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSet", "row_count" ])
+ fstab <- dbGetQuery(dd, "select fsetid from featureSet")
+ checkEquals(nrfs, nrow(fstab))
+
+ if (genomewide){
+ nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSetCNV", "row_count" ])
+ fstab <- dbGetQuery(dd, "select fsetid from featureSetCNV")
+ checkEquals(nrfs, nrow(fstab))
+ }
+
+ }
+
+test_table_info <- function() {
+ ##
+ ## this test verifies that the table_info table knows the correct
+ ## number of rows for featureSet -- commented out a table extraction
+ ##
+ dd <- pdinfo at getdb()
+ tinfo <- dbGetQuery(dd, "select * from table_info")
+ nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSet", "row_count" ])
+# fstab <- dbGetQuery(dd, "select * from featureSet")
+ nrc <- dbGetQuery(dd, "select count(*) from featureSet")[[1]]
+ checkEquals(nrfs, as.numeric(nrc))
+ if (genomewide){
+ nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSetCNV", "row_count" ])
+ fstab <- dbGetQuery(dd, "select fsetid from featureSetCNV")
+ checkEquals(nrfs, nrow(fstab))
+ }
+
+}
+
+test_geom <- function() {
+ dd <- pdinfo at getdb()
+ xylim = pdinfo at geometry
+ xs = dbGetQuery(dd, "select x from pmfeature")[[1]]
+ ys = dbGetQuery(dd, "select y from pmfeature")[[1]]
+ checkTrue(max(xs) <= xylim[2]) # zero offset?
+ checkTrue(max(ys) <= xylim[1]) # zero offset?
+
+ if(genomewide){
+ xs = dbGetQuery(dd, "select x from pmfeatureCNV")[[1]]
+ ys = dbGetQuery(dd, "select y from pmfeatureCNV")[[1]]
+ checkTrue(max(xs) <= xylim[2]) # zero offset?
+ checkTrue(max(ys) <= xylim[1]) # zero offset?
+ }
+}
+
Added: pkg/pd.atdschip.tiling/inst/UnitTests/crlmm_test.R
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/crlmm_test.R (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/crlmm_test.R 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,37 @@
+pdinfo <- "pd.atdschip.tiling"
+
+# the command
+# eg. library(pd.mapping50k.hind240)
+# will have been run in the harness
+
+## test_crlmm <- function() {
+## # this stuff will work for the 4 chips we know about now
+## # 100k hind240, xba240; 250k sty, nsp
+## size = as.character(2*as.numeric(gsub(".*g(.*)k.*", "\\1", pdinfo)))
+## enz = gsub(".*k.(.*$)", "\\1", pdinfo)
+## enz = gsub("240", "", enz)
+## hapmPackName = paste("hapmap", size, "k", enz, sep="")
+## library(oligo)
+## library(hapmPackName, character.only=TRUE)
+## xxr = justSNPRMA(dir(system.file( "celFiles", package=hapmPackName), full=TRUE))
+## xxc = crlmm(xxr, correctionFile="corr.rda")
+## if (exists("xxc")) return(TRUE)
+## return(FALSE)
+## }
+
+test_crlmm <- function(){
+ pkgname <- switch(pdinfo,
+ pd.mapping50k.xba240 = "hapmap100kxba",
+ pd.mapping50k.hind240 = "hapmap100khind",
+ pd.mapping250k.nsp = "hapmap500knsp",
+ pd.mapping250k.sty = "hapmap500ksty",
+ pd.genomewidesnp.5 = "hapmapsnp5",
+ pd.genomewidesnp.6 = "hapmapsnp6")
+ library(oligo)
+ library(pkgname, character.only=TRUE)
+ outdir <- file.path(getwd(), paste(pkgname, "test", sep="_"))
+ celfiles <- list.celfiles(system.file("celFiles", package=pkgname), full=TRUE)
+ result <- crlmm(celfiles, outdir)
+ unlink(outdir, recursive=TRUE)
+ return(result)
+}
Added: pkg/pd.atdschip.tiling/inst/UnitTests/runall.sh
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/runall.sh (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/runall.sh 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+R --slave < runalltests.R
Added: pkg/pd.atdschip.tiling/inst/UnitTests/runalltests.R
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/runalltests.R (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/runalltests.R 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,19 @@
+library("pd.atdschip.tiling")
+library("RUnit")
+
+options(warn=1)
+
+## RUnit Test Suites
+
+dirs <- '.'
+testFilePat <- ".*_test\\.R$"
+
+allSuite <- defineTestSuite(name="Test Suite for pd.atdschip.tiling",
+ dirs=dirs,
+ testFileRegexp=testFilePat,
+ rngKind="default",
+ rngNormalKind="default")
+
+testData <- runTestSuite(allSuite)
+printTextProtocol(testData, showDetails=FALSE)
+
Added: pkg/pd.atdschip.tiling/inst/UnitTests/runfile.sh
===================================================================
--- pkg/pd.atdschip.tiling/inst/UnitTests/runfile.sh (rev 0)
+++ pkg/pd.atdschip.tiling/inst/UnitTests/runfile.sh 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+TEST_FILE=$1
+
+R --slave <<-EOF
+ library('RUnit')
+ library('pd.atdschip.tiling')
+ res <- runTestFile('${TEST_FILE}',
+ rngKind='default', rngNormalKind='default')
+ printTextProtocol(res, showDetails=FALSE)
+EOF
Added: pkg/pd.atdschip.tiling/inst/extdata/pd.atdschip.tiling.sqlite
===================================================================
(Binary files differ)
Property changes on: pkg/pd.atdschip.tiling/inst/extdata/pd.atdschip.tiling.sqlite
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/pd.atdschip.tiling/man/pkg.Rd
===================================================================
--- pkg/pd.atdschip.tiling/man/pkg.Rd (rev 0)
+++ pkg/pd.atdschip.tiling/man/pkg.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,14 @@
+\name{pd.atdschip.tiling}
+\Rdversion{1.1}
+\docType{package}
+\alias{pd.atdschip.tiling}
+\title{
+ Annotation package for pd.atdschip.tiling.
+}
+\description{
+ Annotation package for pd.atdschip.tiling built with pdInfoBuilder.
+}
+\details{
+ This package is to be used in conjunction with the oligo package.
+}
+\keyword{package}
Added: pkg/pd.atdschip.tiling/man/probeSequences.Rd
===================================================================
--- pkg/pd.atdschip.tiling/man/probeSequences.Rd (rev 0)
+++ pkg/pd.atdschip.tiling/man/probeSequences.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,26 @@
+\name{data:pmSequence}
+\Rdversion{1.1}
+\alias{pmSequence}
+\alias{data:pmSequence}
+\alias{bgSequence}
+\alias{data:bgSequence}
+\alias{mmSequence}
+\alias{data:mmSequence}
+\docType{data}
+\title{
+ Sequence data for PM probes.
+}
+\description{
+ Sequence data for PM probes.
+}
+\usage{
+data(pmSequence)
+}
+\format{
+Sequences are stored within an DataFrame object with two columns: 'fid'
+and 'sequence'.
+}
+\examples{
+data(pmSequence)
+}
+\keyword{datasets}
Added: pkg/waveTiling/TODO
===================================================================
--- pkg/waveTiling/TODO (rev 0)
+++ pkg/waveTiling/TODO 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,12 @@
+
+1) plot function: create argument contrasts to plot specific contrasts
+2) wfm.inference: check calculation of confidence intervals
+3) plot: introduce option to give groupnames to put on Y-axis of plot
+4) getNonAnnotatedRegions: make function more generic wrt how the strands and features in the annotation file are defined
+5) getNonAnnotatedRegions: include option to give max./mean expression / FC per region
+6) getNonAnnotatedRegions: add option to set threshold for minimum density of probes within the regions
+7) getSigGenes: add option to include thresholds (density, outliers,...)
+8) getSigGenes: add option to also detect regions that don't overlap but are in the neighbourhood of annotated regions
+9) getSigGenes: add option to include mean / max expression / FC for each gene
+
+
Added: pkg/waveTilingData/DESCRIPTION
===================================================================
--- pkg/waveTilingData/DESCRIPTION (rev 0)
+++ pkg/waveTilingData/DESCRIPTION 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+Package: waveTilingData
+Title: waveTiling Example Data
+Version: 0.1.1
+Created: 2012-02-16
+Author: Kristof De Beuf <kristof.debeuf at ugent.be>
+Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package
+Maintainer: Kristof De Beuf <kristof.debeuf at ugent.be>
+Depends: R (>= 2.14.0)
+License: GPL (>= 2)
+biocViews: Microarray, AnnotationData, ExperimentData
+Packaged:
Added: pkg/waveTilingData/NAMESPACE
===================================================================
--- pkg/waveTilingData/NAMESPACE (rev 0)
+++ pkg/waveTilingData/NAMESPACE 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1 @@
+exportPattern(".")
Added: pkg/waveTilingData/data/leafdev.rda
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Added: pkg/waveTilingData/external_data_store.txt
===================================================================
--- pkg/waveTilingData/external_data_store.txt (rev 0)
+++ pkg/waveTilingData/external_data_store.txt 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1 @@
+data
Added: pkg/waveTilingData/man/leafdev.Rd
===================================================================
--- pkg/waveTilingData/man/leafdev.Rd (rev 0)
+++ pkg/waveTilingData/man/leafdev.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,12 @@
+\name{leafdev}
+\docType{data}
+\alias{leafdev}
+\title{Example data}
+\description{Example data set (\code{TilingFeatureSet}) on leaf development in the plant Arabidopsis thaliana for use of the waveTiling package. The data are taken from [1].}
+\usage{data(leafdev)}
+\references{
+[1] Andriankaja M, Dhondt S, De Bodt S, Vanhaeren H, Coppens F, et al. (2012) Exit from proliferation during leaf development in Arabidopsis thaliana: A not-so-gradual process. Developmental Cell 22: 64-78.}
+\keyword{datasets}
+\examples{
+ data(leafdev)
+}
Added: pkg/waveTilingData/man/leafdevFit.Rd
===================================================================
--- pkg/waveTilingData/man/leafdevFit.Rd (rev 0)
+++ pkg/waveTilingData/man/leafdevFit.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+\name{leafdevFit}
+\docType{data}
+\alias{leafdevFit}
+\title{Example waveTiling fit object}
+\description{Example \code{WfmFit}-class object as output after fitting the wavelet-based functional model to the \code{leafdev} data for the forward strand of chromosome 1.}
+\usage{data(leafdevFit)}
+\references{ }
+\keyword{datasets}
+\examples{
+ data(leafdevFit)
+}
Added: pkg/waveTilingData/man/leafdevInfCompare.Rd
===================================================================
--- pkg/waveTilingData/man/leafdevInfCompare.Rd (rev 0)
+++ pkg/waveTilingData/man/leafdevInfCompare.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+\name{leafdevInfCompare}
+\docType{data}
+\alias{leafdevInfCompare}
+\title{Example waveTiling inference object}
+\description{Example \code{WfmInf}-class object as output after transcriptome analysis of the \code{leafdev} data for the forward strand of chromosome 1, using pairwise comparisons between the different time points.}
+\usage{data(leafdevInfCompare)}
+\references{ }
+\keyword{datasets}
+\examples{
+ data(leafdevInfCompare)
+}
Added: pkg/waveTilingData/man/leafdevMapAndFilterTAIR9.Rd
===================================================================
--- pkg/waveTilingData/man/leafdevMapAndFilterTAIR9.Rd (rev 0)
+++ pkg/waveTilingData/man/leafdevMapAndFilterTAIR9.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+\name{leafdevMapAndFilterTAIR9}
+\docType{data}
+\alias{leafdevMapAndFilterTAIR9}
+\title{Example waveTiling \code{mapFilterProbe} object}
+\description{Example \code{mapFilterProbe}-class object as output after filtering redundant probes (PM/MM and/or forward/reverse strand) and remapping the probes to the Arabidopsis thaliana TAIR9 genome sequence.}
+\usage{data(leafdevMapAndFilterTAIR9)}
+\references{ }
+\keyword{datasets}
+\examples{
+ data(leafdevMapAndFilterTAIR9)
+}
Added: pkg/waveTilingData/man/tair9gff.Rd
===================================================================
--- pkg/waveTilingData/man/tair9gff.Rd (rev 0)
+++ pkg/waveTilingData/man/tair9gff.Rd 2012-05-21 12:46:59 UTC (rev 41)
@@ -0,0 +1,11 @@
+\name{tair9gff}
+\docType{data}
+\alias{tair9gff}
+\title{TAIR 9 Annotation Data}
+\description{TAIR 9 annotation data used in the vignette of the waveTiling package.}
+\usage{data(tair9gff)}
+
+\keyword{datasets}
+\examples{
+ data(tair9gff)
+}
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