some changes

DESCRIPTION

@@ -5,8 +5,8 @@ Version: 0.1.1
 Author: Don Kang <donkang75@gmail.com>
 Maintainer: Don Kang <donkang75@gmail.com>
 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.) For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclustion/exclusion decision.
-Depends: proto, foreach 
-Imports: 
+Depends: R (>= 2.10.0)
+Imports: proto, foreach 
 Suggests: doMC, doSMP, FactoMineR, samr, matrixStats, gdata, gtools
 License: GPL-2
 URL: https://github.com/donkang75/MetaQC

R/MetaQC.R

@@ -2,7 +2,7 @@
 ### DList : list of data set matrices; names should be set
 ### GList : list of gene sets; names should be set // alternatively gmt file also allowed.
 ### isParallel : if multiple core parallel processing will be used (default: TRUE)
-### nCores : how many cores will be used (default: all)
+### nCores : how many cores will be used (default: all in unix-like os and 3 in windows)
 ### useCache : if save GList as cache for next use (default: TRUE)
 ### filterGenes : whether to use gene filtering (recommended to reduce dimension for fast computation)
 MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, filterGenes=TRUE, verbose=FALSE) {
@@ -49,8 +49,6 @@ MetaQC <- function(DList, GList, isParallel=FALSE, nCores=NULL, useCache=TRUE, f
 						.workers <- startWorkers()
 						registerDoSMP(.workers)
 					}
-				} else {
-
 				}
 
 				Cleanup <- function(.) {

man/MetaQC.Rd

@@ -26,7 +26,7 @@ The location of a file which has sets of gene symbol lists such as gmt files. By
 Whether to use multiple cores in parallel for fast computing. By default, it is false.
 }
   \item{nCores}{
-When isParallel is true, the number of cores can be set. By default, all cores in the machine are used.
+When isParallel is true, the number of cores can be set. By default, all cores in the machine are used in the unix-like machine, and 3 cores are used in windows.
 }
   \item{useCache}{
 Whether imported gmt file should be saved for the next use. By default, it is true.

man/requireAll.Rd

@@ -38,9 +38,11 @@ Don Kang (donkang75@gmail.com)
 %% ~~objects to See Also as \code{\link{help}}, ~~~
 }
 \examples{
+	\dontrun{
 	libs <- c("proto", "foreach", ifelse(.Platform$OS.type == "unix", "doMC", "doSMP"))
 	requireAll(libs)
 }
+}
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{ require }