[Robast-commits] r827 - branches/robast-1.0/pkg/RobLoxBioC/man

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

Author: stamats
Date: 2015-05-03 18:03:31 +0200 (Sun, 03 May 2015)
New Revision: 827

Modified:
   branches/robast-1.0/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
   branches/robast-1.0/pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
replaced \dontrun by \donttest

Modified: branches/robast-1.0/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
===================================================================
--- branches/robast-1.0/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd	2015-05-03 16:03:11 UTC (rev 826)
+++ branches/robast-1.0/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd	2015-05-03 16:03:31 UTC (rev 827)
@@ -3,7 +3,7 @@
 \alias{KolmogorovMinDist-methods}
 \alias{KolmogorovMinDist,matrix,Norm-method}
 \alias{KolmogorovMinDist,AffyBatch,AbscontDistribution-method}
-\alias{KolmogorovMinDist,BeadLevelList,AbscontDistribution-method}
+\alias{KolmogorovMinDist,beadLevelData,AbscontDistribution-method}
 
 \title{Generic Function for Computing Minimum Kolmogorov Distance for Biological Data}
 \description{
@@ -17,7 +17,7 @@
 \S4method{KolmogorovMinDist}{AffyBatch,AbscontDistribution}(x, D, bg.correct = TRUE, pmcorrect = TRUE, 
                   verbose = TRUE)
 
-\S4method{KolmogorovMinDist}{BeadLevelList,AbscontDistribution}(x, D, log = FALSE, imagesPerArray = 1, what = "G", 
+\S4method{KolmogorovMinDist}{beadLevelData,AbscontDistribution}(x, D, log = FALSE, what = "Grn", 
                   probes = NULL, arrays = NULL)
 }
 \arguments{
@@ -32,11 +32,8 @@
     If \code{FALSE} only \code{log2(PM)} is used. }
   \item{verbose}{ logical: if \code{TRUE}, some messages are printed. }
   \item{log}{ if \code{TRUE}, then the log2 intensities for each bead-type are summarized. }
-  \item{imagesPerArray}{ Specifies how many images (strips) there are per array. 
-    Normally 1 for a SAM and 1 or 2 for a BeadChip. The images (strips) from the same array 
-    will be combined so that each column in the output represents a sample. }
-  \item{what}{ character string specifying which intensities/values to summarize. 
-    See \code{\link[beadarray]{getArrayData}} for a list of possibilities. }
+  \item{what}{ character string specifying which intensities/values to summarize; 
+    see \code{\link[beadarray]{getBeadData}}. }
   \item{probes}{ Specify particular probes to summarize. If left \code{NULL} then all
     the probes on the first array are used. }
   \item{arrays}{ integer (scalar or vector) specifying the strips/arrays to summarize. 
@@ -68,15 +65,16 @@
 X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
 KolmogorovMinDist(X, D = Norm())
 
-## using Affymetrix-Data
+## using Affymetrix data
 data(SpikeIn)
 probes <- log2(pm(SpikeIn))
 (res <- KolmogorovMinDist(probes, Norm()))
 boxplot(res$dist)
 
-\dontrun{
-## "Not run" just because of computation time
-require(affydata)
+\donttest{
+## \donttest because of check time
+## using Affymetrix data
+library(affydata)
 data(Dilution)
 res <- KolmogorovMinDist(Dilution[,1], Norm())
 summary(res$dist)
@@ -87,14 +85,12 @@
 uni.n <- min(res$n):max(res$n)
 lines(uni.n, 1/(2*uni.n), col = "orange", lwd = 2)
 legend("topright", legend = "minimal possible distance", fill = "orange")
-}
 
-## using Illumina-Data
-\dontrun{
-## "Not run" just because of computation time
-data(BLData)
-res <- KolmogorovMinDist(BLData, Norm(), arrays = 1)
-res1 <- KolmogorovMinDist(BLData, log = TRUE, Norm(), arrays = 1)
+## Illumina bead level data
+library(beadarrayExampleData)
+data(exampleBLData)
+res <- KolmogorovMinDist(exampleBLData, Norm(), arrays = 1)
+res1 <- KolmogorovMinDist(exampleBLData, Norm(), log = TRUE, arrays = 1)
 summary(cbind(res$dist, res1$dist))
 boxplot(list(res$dist, res1$dist), names = c("raw", "log-raw"))
 sort(unique(res1$n))

Modified: branches/robast-1.0/pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- branches/robast-1.0/pkg/RobLoxBioC/man/robloxbioc.Rd	2015-05-03 16:03:11 UTC (rev 826)
+++ branches/robast-1.0/pkg/RobLoxBioC/man/robloxbioc.Rd	2015-05-03 16:03:31 UTC (rev 827)
@@ -147,13 +147,13 @@
 robloxbioc(X, eps = 0.05)
 robloxbioc(X, eps = 0.05, steps = 5)
 
-## Don't run to reduce check time on CRAN
-\dontrun{
+\donttest{
+## \donttest to reduce check time
 ## the function is designed for large scale problems
 X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
 system.time(robloxbioc(X))
 
-## using Affymetrix-Data
+## using Affymetrix data
 ## confer example to generateExprVal.method.mas
 ## A more worked out example can be found in the scripts folder
 ## of the package.
@@ -167,13 +167,15 @@
 points(concentrations, rl[,1], pch = 20, col="orange", type="b")
 legend("topleft", c("MAS", "roblox"), pch = c(1, 20))
 
-require(affydata)
+## Affymetrix dilution data
+library(affydata)
 data(Dilution)
 eset <- robloxbioc(Dilution)
 ## Affymetrix scale normalization
 eset1 <- robloxbioc(Dilution, normalize = TRUE)
-## "Not run" just because of computation time
-require(beadarrayExampleData)
+
+## Illumina bead level data
+library(beadarrayExampleData)
 data(exampleBLData)
 res <- robloxbioc(exampleBLData, eps.upper = 0.5)
 res