version 0.1.8

cran · Jan 16, 2012 · bd58065 · bd58065
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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: 0.1.6
+Version: 0.1.8
 Author: Don Kang <donkang75@gmail.com> and George Tseng
         <ctseng@pitt.edu>
 Maintainer: Don Kang <donkang75@gmail.com>
@@ -32,7 +32,7 @@ License: GPL-2
 URL: https://github.com/donkang75/MetaQC
 LazyLoad: yes
 Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
-Date: 2011-10-17
-Packaged: 2011-10-17 19:08:40 UTC; don
+Date: 2012-01-16
+Packaged: 2012-01-16 05:23:41 UTC; don
 Repository: CRAN
-Date/Publication: 2011-10-18 05:59:12
+Date/Publication: 2012-01-16 07:32:42
diff --git a/MD5 b/MD5
@@ -1,17 +1,17 @@
-62eda68290c7a9a312e37977a8859bff *DESCRIPTION
+90255e6b96799f5426cb64932acfdec9 *DESCRIPTION
 abde996ec487191303de7c015cf694a0 *NAMESPACE
-115b78ebc07a73c1922ab2c4a4055cc6 *R/MetaQC.R
+8a7a74b7075054ef0d3f203f3c381abc *R/MetaQC.R
 045e992b75151a01a136ab0734346e75 *R/cleanup.R
 622edf4b88cff644bc5a5c7f4b215766 *R/functions.R
 747136af145e716b1c9c85cb0a12f7f5 *R/requireAll.R
 b6c2cca24c87e56bd8dd33b8e48b78af *R/runQC.R
 35fa70c4a316424b88aa1ca609d070b1 *data/brain.rda
 ef5a22d59ce52a794593a74f8447e29a *data/datalist
-4fea906710ab5ccff80fa862b815d3bf *man/MetaQC-package.Rd
-c398ff7912e87624b9cd23df341b7105 *man/MetaQC.Rd
+fed180a046f4759c1e98ccaa8e8cbf1d *man/MetaQC-package.Rd
+65b210d4df63e710bd7527c6adf20958 *man/MetaQC.Rd
 b5ec4431932b3841d6b5b48f90d10196 *man/brain.Rd
-c025f1de74a4e2ae4d3d8527c970e71a *man/cleanup.Rd
-16b3a1dfa4bb6712f96ce87e1ef11792 *man/plot.proto.Rd
-0cbfaabae717a1f56b78a21262431240 *man/print.proto.Rd
+96c3b57ac777598e83d7ab2ef36de420 *man/cleanup.Rd
+d762c55478e30e8144a7d4939fb24291 *man/plot.proto.Rd
+e3fbf01f46e2bf413f4eec6c38050c1c *man/print.proto.Rd
 edcab02ebd1cd6ee5c44642838f4f068 *man/requireAll.Rd
-8aeb4121bfc1487f9ad101202d575e24 *man/runQC.Rd
+810a9f25eb3734d6d48ed86a8ec09677 *man/runQC.Rd
diff --git a/R/MetaQC.R b/R/MetaQC.R
@@ -113,10 +113,9 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						.d <- .DListF[[i]]
 						.isNA <- any(is.na(.d))
 
-						.pathMat <- foreach(g=iter(.$.GListIdx[[i]]), .combine=cbind) %dopar% {
-							.pathVec <- rep(0,nrow(.d))
-							.pathVec[g] <- 1
-							return(.pathVec)
+						.pathMat <- matrix(0, nrow(.d), length(.$.GListIdx[[i]]))
+						for(jj in 1:ncol(.pathMat)) {
+							.pathMat[.$.GListIdx[[i]][[jj]], jj] <- 1
 						}
 						rownames(.pathMat) <- 1:nrow(.d) 
 						colnames(.pathMat) <- names(.$.GListIdx[[i]])
@@ -139,6 +138,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						}
 						names(.pathList) <- sapply(.pathList,length)
 
+						#performance significantly degraded by length of .pathList, which is the number of unique pathway sizes
 						.ScoresNullDist <- foreach(b=1:.B, .combine=rbind, .export="printLog") %dopar% {
 
 							.g <- sample(nrow(.pathMat))							
@@ -301,7 +301,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						.dat <- .dat[rowSums(!is.na(.dat))>=3,]
 						.reduced  <- GetEWPval(.dat[,-i])
 						.obs <-  .dat[,i]
-						cor.test(.reduced, .obs, method="spearman", alternative="g")$p.value
+						suppressWarnings(cor.test(.reduced, .obs, method="spearman", alternative="g")$p.value)
 					}
 					names(.$.CQCgScores) <- colnames(.PValMat)
 					.$.CQCgScores <- ifelse(.$.CQCgScores < .Machine$double.xmin, .Machine$double.xmin, .$.CQCgScores)
@@ -356,7 +356,7 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						.dat <- .dat[rowSums(!is.na(.dat))>=3,]
 						.reduced  <- GetEWPval(.dat[,-i])
 						.obs <-  .dat[,i]
-						cor.test(.reduced, .obs, method="spearman")$p.value
+						suppressWarnings(cor.test(.reduced, .obs, method="spearman")$p.value)
 					}
 					names(.$.CQCpScores) <- colnames(.PathPValMat)
 					.$.CQCpScores <- ifelse(.$.CQCpScores < .Machine$double.xmin, .Machine$double.xmin, .$.CQCpScores)
@@ -417,9 +417,10 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 				RunQC <- function(., nPath=NULL, B=1e4, pvalCut=.05, pvalAdjust=FALSE, fileForCQCp="c2.all.v3.0.symbols.gmt", isCAQC=FALSE) {
 					if(!file.exists(fileForCQCp)) {
 						res <- Download("MetaQC",fileForCQCp)
-						if (inherits(res, "try-error") | res != 0L) 
+						if (inherits(res, "try-error") | res != 0L) {
 							file.remove(fileForCQCp)
 							stop(gettextf("download of file '%s' failed!\nPlease download gmt files at http://www.broadinstitute.org/gsea/downloads.jsp", fileForCQCp))
+						} 
 					}
 
 					.GList <- paste(sub("(.+)[.][^.]+$", "\\1", basename(fileForCQCp)),".rda",sep="")

diff --git a/man/MetaQC-package.Rd b/man/MetaQC-package.Rd
@@ -2,7 +2,7 @@
 \alias{MetaQC-package}
 \docType{package}
 \title{
-MetaQC: Quantitative Quality Assessment for Inclusion/Exclusion Criteria of Genomic Meta-Analysis
+MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis
 }
 \description{
 MetaQC implements our proposed quantitative quality control measures: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). (See the reference for detailed explanation.)
@@ -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 0.1.6\cr
-Date: \tab 2011-10-17\cr
+Version: \tab 0.1.8\cr
+Date: \tab 2012-01-16\cr
 License: \tab GPL-2\cr
 LazyLoad: \tab yes\cr
 }
@@ -22,7 +22,7 @@ LazyLoad: \tab yes\cr
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \keyword{ QualityControl }
 \keyword{ MetaAnalysis }% __ONLY ONE__ keyword per line

diff --git a/man/MetaQC.Rd b/man/MetaQC.Rd
@@ -63,7 +63,7 @@ Use Print function to view various information.
 See examples below.
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \author{
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)

diff --git a/man/cleanup.Rd b/man/cleanup.Rd
@@ -26,7 +26,7 @@ A proto R object which obtained by MetaQC function.
 NA
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) Meta-QC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) Meta-QC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \author{
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)

diff --git a/man/plot.proto.Rd b/man/plot.proto.Rd
@@ -29,7 +29,7 @@ Further arguments to print function.
 NA
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \author{
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)

diff --git a/man/print.proto.Rd b/man/print.proto.Rd
@@ -29,7 +29,7 @@ Further arguments to print function.
 NA
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \author{
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)

diff --git a/man/runQC.Rd b/man/runQC.Rd
@@ -42,7 +42,7 @@ Gene set used for CQCp calculation. Usually larger gene set is used than EQC cal
 A data frame showing a summary of each quality control score.
 }
 \references{
-Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (2011) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
+Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. 
 }
 \author{
 Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)