[Robast-commits] r465 - in pkg/RobLoxBioC: R man tests/Examples

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

Author: stamats
Date: 2012-03-03 23:41:04 +0100 (Sat, 03 Mar 2012)
New Revision: 465

Modified:
   pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R
   pkg/RobLoxBioC/man/robloxbioc.Rd
   pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
Log:
it's beadLevelData not BeadLevelData, 
updated function does not work so far!

Modified: pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R
===================================================================
--- pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R	2012-03-03 22:30:52 UTC (rev 464)
+++ pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R	2012-03-03 22:41:04 UTC (rev 465)
@@ -1,4 +1,4 @@
-setMethod("robloxbioc", signature(x = "BeadLevelData"),
+setMethod("robloxbioc", signature(x = "beadLevelData"),
     function(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL, arrays = NULL,
              eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L, 
              fsCor = TRUE, mad0 = 1e-4){

Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd	2012-03-03 22:30:52 UTC (rev 464)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd	2012-03-03 22:41:04 UTC (rev 465)
@@ -3,7 +3,7 @@
 \alias{robloxbioc-methods}
 \alias{robloxbioc,matrix-method}
 \alias{robloxbioc,AffyBatch-method}
-\alias{robloxbioc,BeadLevelData-method}
+\alias{robloxbioc,beadLevelData-method}
 
 \title{Generic Function for Preprocessing Biological Data}
 \description{
@@ -22,7 +22,7 @@
            mad0 = 1e-4, contrast.tau = 0.03, scale.tau = 10, 
            delta = 2^(-20), sc = 500)
 
-\S4method{robloxbioc}{BeadLevelData}(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL, 
+\S4method{robloxbioc}{beadLevelData}(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL, 
            arrays = NULL, eps = NULL, eps.lower = 0, eps.upper = 0.05, 
            steps = 3L, fsCor = TRUE, mad0 = 1e-4)
 }

Modified: pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
===================================================================
--- pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save	2012-03-03 22:30:52 UTC (rev 464)
+++ pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save	2012-03-03 22:41:04 UTC (rev 465)
@@ -347,7 +347,7 @@
 > ### Name: robloxbioc
 > ### Title: Generic Function for Preprocessing Biological Data
 > ### Aliases: robloxbioc robloxbioc-methods robloxbioc,matrix-method
-> ###   robloxbioc,AffyBatch-method robloxbioc,BeadLevelList-method
+> ###   robloxbioc,AffyBatch-method robloxbioc,beadLevelData-method
 > ### Keywords: robust
 > 
 > ### ** Examples
@@ -378,7 +378,7 @@
 > X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
 > system.time(robloxbioc(X))
    user  system elapsed 
-  5.185   0.068   5.274 
+  5.425   0.084   5.528 
 > 
 > ## using Affymetrix-Data
 > ## confer example to generateExprVal.method.mas
@@ -406,11 +406,10 @@
 > ## using Illumina-Data
 > ## Not run: 
 > ##D ## "Not run" just because of computation time
-> ##D if(require(beadarrayExampleData)){
-> ##D   data(exampleBLData)
-> ##D   res <- robloxbioc(exampleBLData, eps.upper = 0.5)
-> ##D   res
-> ##D }
+> ##D require(beadarrayExampleData)
+> ##D data(exampleBLData)
+> ##D res <- robloxbioc(exampleBLData, eps.upper = 0.5)
+> ##D res
 > ## End(Not run)
 > 
 > 
@@ -418,7 +417,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  16.705 0.24 17.152 0 0 
+Time elapsed:  17.865 0.2 18.129 0 0 
 > grDevices::dev.off()
 pdf 
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