[Robast-commits] r960 - in branches/robast-1.1/pkg/RobLoxBioC: . R man

[noreply at r-forge.r-project.org]

Author: ruckdeschel
Date: 2018-07-17 13:20:51 +0200 (Tue, 17 Jul 2018)
New Revision: 960

Modified:
   branches/robast-1.1/pkg/RobLoxBioC/DESCRIPTION
   branches/robast-1.1/pkg/RobLoxBioC/NAMESPACE
   branches/robast-1.1/pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R
   branches/robast-1.1/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
   branches/robast-1.1/pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
[RobLoxBioC] branch 1.1 some URL references to RRlong.pdf updated and some NAMESPACE items added 

Modified: branches/robast-1.1/pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- branches/robast-1.1/pkg/RobLoxBioC/DESCRIPTION	2018-07-17 08:59:47 UTC (rev 959)
+++ branches/robast-1.1/pkg/RobLoxBioC/DESCRIPTION	2018-07-17 11:20:51 UTC (rev 960)
@@ -6,9 +6,9 @@
         estimators for preprocessing omics data, in particular gene expression data.
 Depends: R(>= 2.14.0), methods, distr(>= 2.5.2), affy
 Imports: Biobase, BiocGenerics, beadarray, RobLox(>= 0.9.2), distrMod(>= 2.5.2), lattice,
-        RColorBrewer
+        RColorBrewer, AnnotationDbi
 Suggests: affydata, hgu95av2cdf, beadarrayExampleData, illuminaHumanv3.db
-Authors at R: person("Matthias", "Kohl", role=c("cre", "cph"), email="Matthias.Kohl at stamats.de")
+Authors at R: person("Matthias", "Kohl", role=c("aut", "cre", "cph"), email="Matthias.Kohl at stamats.de")
 ByteCompile: yes
 License: LGPL-3
 URL: http://robast.r-forge.r-project.org/

Modified: branches/robast-1.1/pkg/RobLoxBioC/NAMESPACE
===================================================================
--- branches/robast-1.1/pkg/RobLoxBioC/NAMESPACE	2018-07-17 08:59:47 UTC (rev 959)
+++ branches/robast-1.1/pkg/RobLoxBioC/NAMESPACE	2018-07-17 11:20:51 UTC (rev 960)
@@ -4,12 +4,20 @@
 importFrom("lattice","stripplot")
 importMethodsFrom("BiocGenerics","append","annotation")
 importFrom("Biobase","assayDataNew")
+importFrom("AnnotationDbi", "revmap")
 importClassesFrom("Biobase","ExpressionSet","AssayData","AnnotatedDataFrame")
 importMethodsFrom("Biobase", "rowMedians", "featureNames", "sampleNames", 
-           "phenoData", "experimentData", "exprs", "exprs<-", "assayData","assayData<-")
+           "phenoData", "experimentData", "exprs", "exprs<-", "assayData","assayData<-",
+		   "featureData<-", "phenoData<-")
 importFrom("affy","bg.correct.mas","getCdfInfo", "tukey.biweight")
 importMethodsFrom("affy","intensity")
+importMethodsFrom("AnnotationDbi", "mappedkeys")
 import("beadarray")
 importFrom("RobLox", "rowRoblox", "finiteSampleCorrection")
+importFrom("grDevices", "dev.new")
+importFrom("graphics", "abline", "curve", "layout", "legend", "par")
+importFrom("stats", "optim", "pnorm", "qnorm", "rbinom", "rnorm",
+             "uniroot")
+importFrom("utils", "packageDescription")
 exportMethods("robloxbioc", "KolmogorovMinDist")
 export("AffySimStudy", "IlluminaSimStudy")

Modified: branches/robast-1.1/pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R
===================================================================
--- branches/robast-1.1/pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R	2018-07-17 08:59:47 UTC (rev 959)
+++ branches/robast-1.1/pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R	2018-07-17 11:20:51 UTC (rev 960)
@@ -181,7 +181,7 @@
                 rownames(eMat) <- rownames(varMat) <- rownames(nObs) <- as.character(IlluminaIDs)
                 status <- rep("Unknown", length(probeIDs))
                 annoPkg <- paste("illumina", annoName, ".db", sep = "")
-                annoVers <- packageDescription(annoPkg, field = "Version")
+                annoVers <- packageDescription(annoPkg, fields = "Version")
                 message(paste("Annotating control probes using package ", annoPkg, " Version:", annoVers, "\n", sep = ""))
                 mapEnv <- as.name(paste("illumina", annoName, "REPORTERGROUPNAME", sep = ""))
                 t <- try(eval(mapEnv), silent = TRUE)

Modified: branches/robast-1.1/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
===================================================================
--- branches/robast-1.1/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd	2018-07-17 08:59:47 UTC (rev 959)
+++ branches/robast-1.1/pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd	2018-07-17 11:20:51 UTC (rev 960)
@@ -43,7 +43,7 @@
 
   Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
   the Radius. \emph{Statistical Methods and Applications} \bold{17}(1) 13-40.
-  Extended version: \url{http://www.stamats.de/RRlong.pdf}
+  Extended version: \url{http://r-kurs.de/RRlong.pdf}
 }
 \seealso{
 \code{\link[RobLox]{roblox}}, \code{\link[RobLox]{rowRoblox}}

Modified: branches/robast-1.1/pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- branches/robast-1.1/pkg/RobLoxBioC/man/robloxbioc.Rd	2018-07-17 08:59:47 UTC (rev 959)
+++ branches/robast-1.1/pkg/RobLoxBioC/man/robloxbioc.Rd	2018-07-17 11:20:51 UTC (rev 960)
@@ -125,7 +125,7 @@
 
   Rieder, H., Kohl, M. and Ruckdeschel, P. (2008) The Costs of not Knowing
   the Radius. \emph{Statistical Methods and Applications} \bold{17}(1) 13-40.
-  Extended version: \url{http://www.stamats.de/RRlong.pdf}
+  Extended version: \url{http://r-kurs.de/RRlong.pdf}
 }
 \author{Matthias Kohl \email{Matthias.Kohl at stamats.de},