[Robast-commits] r398 - in pkg/RobLoxBioC: . R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 1 15:29:53 CEST 2010
Author: stamats
Date: 2010-04-01 15:29:53 +0200 (Thu, 01 Apr 2010)
New Revision: 398
Modified:
pkg/RobLoxBioC/DESCRIPTION
pkg/RobLoxBioC/R/AffySimStudyFunction.R
pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R
pkg/RobLoxBioC/inst/NEWS
pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
pkg/RobLoxBioC/man/robloxbioc.Rd
pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
Log:
some minor modifications
Modified: pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- pkg/RobLoxBioC/DESCRIPTION 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/DESCRIPTION 2010-04-01 13:29:53 UTC (rev 398)
@@ -1,6 +1,6 @@
Package: RobLoxBioC
Version: 0.7.1
-Date: 2010-02-23
+Date: 2010-04-01
Title: Infinitesimally robust estimators for preprocessing omics data
Description: Functions for the determination of optimally robust influence curves and estimators for preprocessing omics data, in
particular gene expression data.
Modified: pkg/RobLoxBioC/R/AffySimStudyFunction.R
===================================================================
--- pkg/RobLoxBioC/R/AffySimStudyFunction.R 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/R/AffySimStudyFunction.R 2010-04-01 13:29:53 UTC (rev 398)
@@ -41,7 +41,7 @@
ind <- sample(1:M, min(M, 20))
if(plot1) dev.new()
print(
- stripplot(rep(1:20, each = 20) ~ as.vector(Mre[ind,]),
+ stripplot(rep(1:min(M, 20), each = n) ~ as.vector(Mre[ind,]),
ylab = "samples", xlab = "x", pch = 20,
main = "Randomly chosen samples")
)
Modified: pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R
===================================================================
--- pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R 2010-04-01 13:29:53 UTC (rev 398)
@@ -42,7 +42,7 @@
ind <- sample(1:M, min(M, 20))
if(plot1) dev.new()
print(
- stripplot(rep(1:20, each = 20) ~ as.vector(Mre[ind,]),
+ stripplot(rep(1:min(M, 20), each = n) ~ as.vector(Mre[ind,]),
ylab = "samples", xlab = "x", pch = 20,
main = "Randomly chosen samples")
)
Modified: pkg/RobLoxBioC/inst/NEWS
===================================================================
--- pkg/RobLoxBioC/inst/NEWS 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/inst/NEWS 2010-04-01 13:29:53 UTC (rev 398)
@@ -8,10 +8,16 @@
information)
#######################################
-version 0.7
+## version 0.7.1
#######################################
++ corrected bug in AffySimStudy and IlluminaSimStudy
++ minor modifications of scripts in scripts folder
+#######################################
+## version 0.7
+#######################################
+
GENERAL ENHANCEMENTS:
+ added tests/Examples folder with file RobLoxBioC-Ex.Rout.save to have
@@ -53,14 +59,14 @@
#######################################
-version 0.5
+## version 0.5
#######################################
+ added example code for Illumina data
+ function to perform Monte-Carlo studies for comparison with Illumina's
default method
#######################################
-version 0.4
+## version 0.4
#######################################
+ added finite-sample correction
+ handle cases with sample size <= 2 and contamination eps = 0
@@ -68,17 +74,17 @@
exported and documented function to perform Monte-Carlo studies.
#######################################
-version 0.3
+## version 0.3
#######################################
+ added KolmogorovMinDist methods for matrix, AffyBatch and BeadLevelList
#######################################
-version 0.2
+## version 0.2
#######################################
+ robloxbioc methods for AffyBatch and BeadLevelList
#######################################
-version 0.1
+## version 0.1
#######################################
+ start of development
Modified: pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd
===================================================================
--- pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/man/0RobLoxBioC-package.Rd 2010-04-01 13:29:53 UTC (rev 398)
@@ -13,7 +13,7 @@
\tabular{ll}{
Package: \tab RobLoxBioC \cr
Version: \tab 0.7.1 \cr
-Date: \tab 2010-02-23 \cr
+Date: \tab 2010-04-01 \cr
Depends: \tab R(>= 2.8.1), methods, Biobase, affy, beadarray, distr, RobLox, lattice, RColorBrewer \cr
LazyLoad: \tab yes \cr
License: \tab LGPL-3 \cr
Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd 2010-04-01 13:29:53 UTC (rev 398)
@@ -131,9 +131,9 @@
ind <- rbinom(200, size=1, prob=0.05)
X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
robloxbioc(X)
-robloxbioc(X, steps = 3)
+robloxbioc(X, steps = 5)
robloxbioc(X, eps = 0.05)
-robloxbioc(X, eps = 0.05, steps = 3)
+robloxbioc(X, eps = 0.05, steps = 5)
## the function is designed for large scale problems
X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
Modified: pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
===================================================================
--- pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2010-03-15 01:24:44 UTC (rev 397)
+++ pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2010-04-01 13:29:53 UTC (rev 398)
@@ -1,6 +1,6 @@
-R version 2.10.0 beta (2009-10-15 r50107)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.10.1 Patched (2010-03-27 r51528)
+Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -17,73 +17,8 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-> ### * <HEADER>
-> ###
-> attach(NULL, name = "CheckExEnv")
-> assign("nameEx",
-+ local({
-+ s <- "__{must remake R-ex/*.R}__"
-+ function(new) {
-+ if(!missing(new)) s <<- new else s
-+ }
-+ }),
-+ pos = "CheckExEnv")
-> ## Add some hooks to label plot pages for base and grid graphics
-> assign("base_plot_hook",
-+ function() {
-+ pp <- par(c("mfg","mfcol","oma","mar"))
-+ if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
-+ outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4]
-+ mtext(sprintf("help(\"%s\")", nameEx()), side = 4,
-+ line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
-+ outer = outer, adj = 1, cex = .8, col = "orchid", las=3)
-+ }
-+ },
-+ pos = "CheckExEnv")
-> assign("grid_plot_hook",
-+ function() {
-+ grid::pushViewport(grid::viewport(width=grid::unit(1, "npc") -
-+ grid::unit(1, "lines"), x=0, just="left"))
-+ grid::grid.text(sprintf("help(\"%s\")", nameEx()),
-+ x=grid::unit(1, "npc") + grid::unit(0.5, "lines"),
-+ y=grid::unit(0.8, "npc"), rot=90,
-+ gp=grid::gpar(col="orchid"))
-+ },
-+ pos = "CheckExEnv")
-> setHook("plot.new", get("base_plot_hook", pos = "CheckExEnv"))
-> setHook("persp", get("base_plot_hook", pos = "CheckExEnv"))
-> setHook("grid.newpage", get("grid_plot_hook", pos = "CheckExEnv"))
-> assign("cleanEx",
-+ function(env = .GlobalEnv) {
-+ rm(list = ls(envir = env, all.names = TRUE), envir = env)
-+ RNGkind("default", "default")
-+ set.seed(1)
-+ options(warn = 1)
-+ .CheckExEnv <- as.environment("CheckExEnv")
-+ delayedAssign("T", stop("T used instead of TRUE"),
-+ assign.env = .CheckExEnv)
-+ delayedAssign("F", stop("F used instead of FALSE"),
-+ assign.env = .CheckExEnv)
-+ sch <- search()
-+ newitems <- sch[! sch %in% .oldSearch]
-+ for(item in rev(newitems))
-+ eval(substitute(detach(item), list(item=item)))
-+ missitems <- .oldSearch[! .oldSearch %in% sch]
-+ if(length(missitems))
-+ warning("items ", paste(missitems, collapse=", "),
-+ " have been removed from the search path")
-+ },
-+ pos = "CheckExEnv")
-> assign("ptime", proc.time(), pos = "CheckExEnv")
-> ## at least one package changes these via ps.options(), so do this
-> ## before loading the package.
-> ## Use postscript as incomplete files may be viewable, unlike PDF.
-> ## Choose a size that is close to on-screen devices, fix paper
-> grDevices::ps.options(width = 7, height = 7, paper = "a4", reset = TRUE)
-> grDevices::postscript("RobLoxBioC-Ex.ps")
->
-> assign("par.postscript", graphics::par(no.readonly = TRUE), pos = "CheckExEnv")
-> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
+> pkgname <- "RobLoxBioC"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('RobLoxBioC')
Loading required package: Biobase
@@ -104,37 +39,8 @@
:startupmsg> NEWS("startupmsg")
Loading required package: sfsmisc
-Loading required package: SweaveListingUtils
-:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version 0.4)
-:SweaveListingUtils>
-:SweaveListingUtils> Some functions from package 'base'
-:SweaveListingUtils> are intentionally masked ---see
-:SweaveListingUtils> SweaveListingMASK().
-:SweaveListingUtils>
-:SweaveListingUtils> Note that global options are
-:SweaveListingUtils> controlled by
-:SweaveListingUtils> SweaveListingoptions() ---c.f.
-:SweaveListingUtils> ?"SweaveListingoptions".
-:SweaveListingUtils>
-:SweaveListingUtils> For more information see
-:SweaveListingUtils> ?"SweaveListingUtils",
-:SweaveListingUtils> NEWS("SweaveListingUtils")
-:SweaveListingUtils> There is a vignette to this
-:SweaveListingUtils> package; try
-:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
-
-
-Attaching package: 'SweaveListingUtils'
-
-
- The following object(s) are masked from package:base :
-
- library,
- require
-
:distr> Object orientated implementation of distributions (version
-:distr> 2.2)
+:distr> 2.2.2)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -239,7 +145,7 @@
confint
Loading required package: RobAStBase
-:RobAStBase> Robust Asymptotic Statistics (version 0.7)
+:RobAStBase> Robust Asymptotic Statistics (version 0.7.1)
:RobAStBase>
:RobAStBase> Some functions from pkg's 'stats' and 'graphics'
:RobAStBase> are intentionally masked ---see RobAStBaseMASK().
@@ -276,8 +182,8 @@
Loading required package: RColorBrewer
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
-> assign(".oldNS", loadedNamespaces(), pos = 'CheckExEnv')
-> cleanEx(); nameEx("0RobLoxBioC-package")
+> cleanEx()
+> nameEx("0RobLoxBioC-package")
> ### * 0RobLoxBioC-package
>
> flush(stderr()); flush(stdout())
@@ -293,7 +199,8 @@
>
>
>
-> cleanEx(); nameEx("KolmogorovMinDist")
+> cleanEx()
+> nameEx("KolmogorovMinDist")
> ### * KolmogorovMinDist
>
> flush(stderr()); flush(stdout())
@@ -325,8 +232,8 @@
> probes <- log2(pm(SpikeIn))
> (res <- KolmogorovMinDist(probes, Norm()))
$dist
- [1] 0.1755693 0.1567648 0.1571410 0.1609188 0.1617499 0.1607157 0.1382646
- [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1729001 0.1519412
+ [1] 0.1642185 0.1567706 0.1571387 0.1609188 0.1617499 0.1607157 0.1382646
+ [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1728984 0.1519412
[15] 0.1682097 0.1662173 0.1547481 0.1716497 0.1751219 0.1671566
$n
@@ -368,7 +275,8 @@
>
>
>
-> cleanEx(); nameEx("SimStudies")
+> cleanEx()
+> nameEx("SimStudies")
> ### * SimStudies
>
> flush(stderr()); flush(stdout())
@@ -382,46 +290,6 @@
>
> AffySimStudy(n = 11, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
+ plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
dev.new(): using pdf(file="Rplots1.pdf")
ML Med Tukey rmx
n x empMSE (loc) 1.2837045 1.826711 1.698428 1.399230
@@ -433,86 +301,6 @@
> IlluminaSimStudy(n = 30, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
+ plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
dev.new(): using pdf(file="Rplots2.pdf")
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) :
- longer object length is not a multiple of shorter object length
-Warning in id & (y >= levels(y)[[k]][1]) & (y <= levels(y)[[k]][2]) :
- longer object length is not a multiple of shorter object length
dev.new(): using pdf(file="Rplots3.pdf")
ML Med Illumina rmx
n x empMSE (loc) 1.172077 1.591148 1.205941 1.1132052
@@ -524,7 +312,8 @@
>
>
>
-> cleanEx(); nameEx("robloxbioc")
+> cleanEx()
+> nameEx("robloxbioc")
> ### * robloxbioc
>
> flush(stderr()); flush(stdout())
@@ -544,24 +333,24 @@
mean sd
[1,] -0.014713379 0.9643588
[2,] 0.003050954 1.0587182
-> robloxbioc(X, steps = 3)
+> robloxbioc(X, steps = 5)
mean sd
-[1,] -0.014713379 0.9643588
-[2,] 0.003050954 1.0587182
+[1,] -0.014294296 0.9649008
+[2,] 0.003004433 1.0587286
> robloxbioc(X, eps = 0.05)
mean sd
[1,] -0.028278572 0.927434
[2,] -0.001566506 1.051123
-> robloxbioc(X, eps = 0.05, steps = 3)
- mean sd
-[1,] -0.028278572 0.927434
-[2,] -0.001566506 1.051123
+> robloxbioc(X, eps = 0.05, steps = 5)
+ mean sd
+[1,] -0.028227242 0.9276155
+[2,] -0.001567355 1.0511232
>
> ## the function is designed for large scale problems
> X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
> system.time(robloxbioc(X))
user system elapsed
- 6.196 0.112 6.311
+ 11.692 0.888 14.859
>
> ## using Affymetrix-Data
> ## confer example to generateExprVal.method.mas
@@ -598,7 +387,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 15.1 0.24 15.41 0.004 0.004
+Time elapsed: 29.937 1.044 35.693 0.016 0.008
> grDevices::dev.off()
postscript
2
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