Rd file 'MetaPCA-package.Rd':
  \examples lines wider than 100 characters:
                     plot(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], type="n", xlab="", ylab="", xaxt="n", yaxt="n")
                     text(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], 1:nrow(metaPC$x[[i]]$coord), cex=1.5)
             PlotPC2D(coord[,1:2], drawEllipse=F, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"), 
                             .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))), 
             #In the case of "SparseAngle" method, the top contributing genes for all studies can be determined

Rd file 'MetaPCA.Rd':
  \usage lines wider than 90 characters:
     MetaPCA(DList, method=c("Angle","Eigen","RobustAngle","SparseAngle"), robust.var=c("qn","mad"), nPC=2,
                             .weight=rep(1/length(DList),length(DList)), sparse.maxFeatures=NULL, sparse.lambda=NULL, 
                             sparse.max.iter=100, sparse.eps=1e-3, .scale=FALSE, .scaleAdjust=TRUE, doPreprocess=TRUE, 
                             cutRatioByMean=.4, cutRatioByVar=.4, doImpute=TRUE,     na.rm.pct=.1, na.rm.pct.each=.5, 
  \examples lines wider than 100 characters:
                     plot(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], type="n", xlab="", ylab="", xaxt="n", yaxt="n")
                     text(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], 1:nrow(metaPC$x[[i]]$coord), cex=1.5)
             PlotPC2D(coord[,1:2], drawEllipse=F, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"), 
                             .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))), 
             #In the case of "SparseAngle" method, the top contributing genes for all studies can be determined

Rd file 'PlotPC2D.Rd':
  \usage lines wider than 90 characters:
                     .points.size=1, .class=rownames(coord), .class.order=NULL, .class.color=NULL, 
                     .legend=c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"))
  \examples lines wider than 100 characters:
             PlotPC2D(coord[,1:2], drawEllipse=T, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"), 
                             .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))), 

Rd file 'PreprocessMetaAnalysis.Rd':
  \usage lines wider than 90 characters:
     PreprocessMetaAnalysis(DList, cutRatioByMean=.4, cutRatioByVar=.4, doImpute=FALSE, na.rm.pct=.1, na.rm.pct.each=.5, verbose=FALSE)
  \examples lines wider than 100 characters:
     DList <- PreprocessMetaAnalysis(list(Yu=Yu, Lapointe=Lapointe, Tomlins=Tomlins, Varambally=Varambally), 

These lines will be truncated in the PDF manual.