version 0.1.9

cran · Feb 25, 2012 · 60c509f · 60c509f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: MetaQC
 Type: Package
 Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
         Criteria for Genomic Meta-Analysis
-Version: 0.1.8
+Version: 0.1.9
 Author: Don Kang <donkang75@gmail.com> and George Tseng
         <ctseng@pitt.edu>
 Maintainer: Don Kang <donkang75@gmail.com>
@@ -27,12 +27,12 @@ Description: MetaQC implements our proposed quantitative quality
         preprocessing etc) of their bad quality or irreproducibility
         for final inclustion/exclusion decision.
 Depends: R (>= 2.10.0), proto, foreach
-Suggests: doMC, doSMP, FactoMineR, samr, matrixStats, gdata, gtools
+Suggests: doMC, doSNOW, FactoMineR, samr, matrixStats, gdata, gtools
 License: GPL-2
 URL: https://github.com/donkang75/MetaQC
 LazyLoad: yes
 Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
-Date: 2012-01-16
-Packaged: 2012-01-16 05:23:41 UTC; don
+Date: 2012-02-25
+Packaged: 2012-02-26 07:33:24 UTC; don
 Repository: CRAN
-Date/Publication: 2012-01-16 07:32:42
+Date/Publication: 2012-02-26 16:31:52
diff --git a/MD5 b/MD5
@@ -1,17 +1,17 @@
-90255e6b96799f5426cb64932acfdec9 *DESCRIPTION
+c8e0fe79550f0661b4aab85491df4ab2 *DESCRIPTION
 abde996ec487191303de7c015cf694a0 *NAMESPACE
-8a7a74b7075054ef0d3f203f3c381abc *R/MetaQC.R
-045e992b75151a01a136ab0734346e75 *R/cleanup.R
-622edf4b88cff644bc5a5c7f4b215766 *R/functions.R
+08b13788babc860f8d740a2970d1635f *R/MetaQC.R
+98f4ebfcc928281f6a0dc3c995cdf581 *R/cleanup.R
+6adfded4a7857fdbb42531c262478166 *R/functions.R
 747136af145e716b1c9c85cb0a12f7f5 *R/requireAll.R
 b6c2cca24c87e56bd8dd33b8e48b78af *R/runQC.R
 35fa70c4a316424b88aa1ca609d070b1 *data/brain.rda
 ef5a22d59ce52a794593a74f8447e29a *data/datalist
-fed180a046f4759c1e98ccaa8e8cbf1d *man/MetaQC-package.Rd
-65b210d4df63e710bd7527c6adf20958 *man/MetaQC.Rd
+3a4f0e774a66acf873ef10551a101b4e *man/MetaQC-package.Rd
+4c3a49c04c8b2bddb9044abaaf749333 *man/MetaQC.Rd
 b5ec4431932b3841d6b5b48f90d10196 *man/brain.Rd
-96c3b57ac777598e83d7ab2ef36de420 *man/cleanup.Rd
-d762c55478e30e8144a7d4939fb24291 *man/plot.proto.Rd
-e3fbf01f46e2bf413f4eec6c38050c1c *man/print.proto.Rd
-edcab02ebd1cd6ee5c44642838f4f068 *man/requireAll.Rd
-810a9f25eb3734d6d48ed86a8ec09677 *man/runQC.Rd
+8f98d634094ea142e5061af5de5ecd02 *man/cleanup.Rd
+a7eb00ce06c12217b96171385f942af6 *man/plot.proto.Rd
+a68a6fc7f3e513d04f12165f830001f6 *man/print.proto.Rd
+d88335fc48896e46c0c53df353117546 *man/requireAll.Rd
+fd5de5896115c100df99989d335eac9d *man/runQC.Rd
diff --git a/R/MetaQC.R b/R/MetaQC.R
@@ -46,17 +46,20 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						requireAll("doMC")
 						registerDoMC()
 					} else { #windows
-						requireAll("doSMP")
+						requireAll("doSNOW")
 						if(is.null(getOption('cores')))
 							options(cores=2)
-						.workers <- startWorkers()
-						registerDoSMP(.workers)
+						registerDoSNOW(makeCluster(getOption('cores'), type = "SOCK"))
+						#.workers <- startWorkers()
+						#registerDoSMP(.workers)
 					}
 				}
 
 				Cleanup <- function(.) {
-					if(!is.null(.$.workers))
-						stopWorkers(.$.workers)
+					warning("This function was deprecated.\n",
+							"No more needed to call this function.\n")
+#					if(!is.null(.$.workers))
+#						stopWorkers(.$.workers)
 				}
 
 				.Initialize <- function(., .DList, .GList, .filterGenes) {
@@ -87,7 +90,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 				}
 
 				.ConvertToGeneSetIdx <- function(., .DListF=.$.DListF, .GList=.$.GList, .minNumGenes=.$.minNumGenes) {
-					.DGList <- foreach(d=iter(.DListF)) %dopar% { #each data set wrap each pathway
+					.DGList <- foreach(d=iter(.DListF), .packages="foreach") %dopar% { #each data set wrap each pathway
 						.res <- foreach(g=iter(.GList)) %do% {
 							.gs <- na.omit(match(g, rownames(d)))
 							if(length(.gs)<.minNumGenes) return(NA)
@@ -327,7 +330,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 					if(is.null(.$.PathPValMat)) {
 						load(.GList)
 						.GListIdx <- .$.ConvertToGeneSetIdx(.GList=GList)
-						.PathPValList <- foreach(ii=1:length(.GListIdx)) %dopar% {
+						.PathPValList <- foreach(ii=1:length(.GListIdx), .packages="foreach") %dopar% {
 							.PathPVal <- foreach(jj=iter(.GListIdx[[ii]]), .combine=c) %do% {
 								.gnInPath <- rownames(.$.DListF[[ii]])[jj] #gene names in the pathway
 								.gMatched <- sort(match(.gnInPath, rownames(.$.PValMat0)))
@@ -390,7 +393,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 				.CalcDistOfStudies <- function(.) {
 					stopifnot(!is.null(.$.DListF))
 
-					.$.DistOfStudies <- foreach(ii=iter(combinations(length(.$.DListF),2),by="row"), .combine=c) %dopar% {
+					.$.DistOfStudies <- foreach(ii=iter(combinations(length(.$.DListF),2),by="row"), .combine=c, .packages="foreach") %dopar% {
 						.gn <- intersect(rownames(.$.DListF[[ii[1]]]),rownames(.$.DListF[[ii[2]]]))
 
 						.DistOfStudies <- foreach(1:100, .combine=c) %do% { #resampling based to fit practical memory limit

diff --git a/R/cleanup.R b/R/cleanup.R
@@ -1,4 +1,6 @@
 cleanup <- function(QC) {
-	if(!is.null(QC$.workers))
-		stopWorkers(QC$.workers)
+	warning("This function was deprecated.\n",
+			"No more needed to call this function.\n")
+#	if(!is.null(QC$.workers))
+#		stopWorkers(QC$.workers)
 }
diff --git a/R/functions.R b/R/functions.R
@@ -104,6 +104,10 @@ rowVars <- function (x, center = NULL, ...) {
 }
 
 GMT2List <- function(f, saveAs=NULL) {
+	trim <- function(x) {
+		sub(" +$", "", sub("^ +", "", x))
+	}
+
 	con <- file(f, "r", blocking = FALSE)
 	GList <- readLines(con) # empty
 	GList <- lapply(GList, function(x) unlist(strsplit(x, "\t", fixed=T)))
@@ -117,10 +121,6 @@ GMT2List <- function(f, saveAs=NULL) {
 	return(GList)
 }
 
-trim <- function(x) {
-	sub(" +$", "", sub("^ +", "", x))
-}
-
 getFileExt <- function(x) {
 	sub(".*[.]", "", x)
 }

diff --git a/man/MetaQC-package.Rd b/man/MetaQC-package.Rd
@@ -12,8 +12,8 @@ For each quality control index, the p-values from statistical hypothesis testing
 \tabular{ll}{
 Package: \tab MetaQC\cr
 Type: \tab Package\cr
-Version: \tab 0.1.8\cr
-Date: \tab 2012-01-16\cr
+Version: \tab 0.1.9\cr
+Date: \tab 2012-02-25\cr
 License: \tab GPL-2\cr
 LazyLoad: \tab yes\cr
 }
@@ -52,7 +52,6 @@ Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nuclei
     #B is recommended to be >= 1e4 in real application
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
     ## For parallel computation with all cores
 	## In windows, only 2 cores are used if not specified explicitly
@@ -61,7 +60,6 @@ Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nuclei
 	#B is recommended to be >= 1e4 in real application					
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 	## Real Example which is used in the paper
 	#download the brainFull file 
@@ -71,7 +69,6 @@ Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nuclei
 			verbose=TRUE, isParallel=TRUE)
     runQC(brainQC, B=1e4, fileForCQCp="c2.all.v3.0.symbols.gmt") #B was 1e5 in the paper
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 }
 }
diff --git a/man/MetaQC.Rd b/man/MetaQC.Rd
@@ -100,7 +100,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
     #B is recommended to be >= 1e4 in real application
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
     ## For parallel computation with all cores
 	## In windows, only 2 cores are used if not specified explicitly
@@ -109,7 +108,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 	#B is recommended to be >= 1e4 in real application					
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 	## Real Example which is used in the paper
 	#download the brainFull file 
@@ -119,7 +117,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 			verbose=TRUE, isParallel=TRUE)
     runQC(brainQC, B=1e4, fileForCQCp="c2.all.v3.0.symbols.gmt") #B was 1e5 in the paper
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 }
 }

diff --git a/man/cleanup.Rd b/man/cleanup.Rd
@@ -6,7 +6,7 @@ Cleaning up resources.
 }
 
 \description{
-It is to shutdown the workers used for parallel processing and release resources. It is only necessary in windows.
+It is to shutdown the workers used for parallel processing and release resources. It is only necessary in windows. (Deprecated)
 }
 
 \usage{

diff --git a/man/plot.proto.Rd b/man/plot.proto.Rd
@@ -10,7 +10,7 @@ It draws a PCA biplot which shows the four QC measures. CQCg and AQCg are combin
 }
 
 \usage{
-plot.proto(x, ...)
+\method{plot}{proto}(x, \dots)
 }
 
 \arguments{

diff --git a/man/print.proto.Rd b/man/print.proto.Rd
@@ -10,7 +10,7 @@ It prints out the results of all QC measures and standardized mean rank of each
 }
 
 \usage{
-print.proto(x, ...)
+\method{print}{proto}(x, \dots)
 }
 
 \arguments{

diff --git a/man/requireAll.Rd b/man/requireAll.Rd
@@ -40,7 +40,7 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 \examples{
 	\dontrun{
 	    libs <- c("proto", "foreach", ifelse(.Platform$OS.type == "unix", 
-					"doMC", "doSMP")) #doSMP is available to R > 2.11.0
+					"doMC", "doSNOW")) 
 	    requireAll(libs)
 }
 }

diff --git a/man/runQC.Rd b/man/runQC.Rd
@@ -80,7 +80,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
     #B is recommended to be >= 1e4 in real application
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
     ## For parallel computation with all cores
 	## In windows, only 2 cores are used if not specified explicitly
@@ -89,7 +88,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 	#B is recommended to be >= 1e4 in real application					
     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 	## Real Example which is used in the paper
 	#download the brainFull file 
@@ -99,7 +97,6 @@ Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 			verbose=TRUE, isParallel=TRUE)
     runQC(brainQC, B=1e4, fileForCQCp="c2.all.v3.0.symbols.gmt") #B was 1e5 in the paper
     plot(brainQC)
-    cleanup(brainQC) #neccessary for windows after using parallel processing
 
 }
 }