Rd file 'MAP.Matches.Rd':
  \usage lines wider than 90 characters:
     MAP.Matches(data, varname, t.cutoff = "98.00%", multiple = TRUE, perm = c("both", "columns", "labels")[1], nperm = 1000, test = c("t",  ... [TRUNCATED]

Rd file 'RandomScore.Rd':
  \usage lines wider than 90 characters:
     RandomScore(data, varname, B, alpha, test, which = c("random", "empirical", "subsample"), two.sided = TRUE)

Rd file 'RankProduct.Rd':
  \usage lines wider than 90 characters:
     RankProduct(data, varname, num.perm = 100, logged = TRUE, na.rm = FALSE, gene.names = NULL, plot = FALSE, rand = NULL, cutoff = 0.05)

Rd file 'Z.Rd':
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'conting.tab.Rd':
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'entitybuild2.Rd':
  \usage lines wider than 90 characters:
     entitybuild2(expr.mat, ALLtype = NULL, type, dataset = NULL, minSampleNum = 3, method = "t", random = FALSE)

Rd file 'fold.change.Rd':
  \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),

Rd file 'gene.list.Rd':
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'gene.select.FC.Rd':
  \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),

Rd file 'make.matrix.Rd':
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'metaMA.Rd':
  \usage lines wider than 90 characters:
     metaMA(data, varname, moderated = c("limma", "SMVar", "t")[1], BHth = 0.05, which = c("pval", "ES")[1])

Rd file 'metaheat.Rd':
  \usage lines wider than 90 characters:
     metaheat(x, Rowv = NA, Colv = NA, distfun = dist, hclustfun = hclust, na.rm = TRUE, do.dendro = c(TRUE, TRUE), legend = 0, legfrac = 8, ... [TRUNCATED]
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'metaheat2.Rd':
  \usage lines wider than 90 characters:
     metaheat2(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both", "row", "column" ... [TRUNCATED]

Rd file 'performSOGL.Rd':
  \usage lines wider than 90 characters:
     performSOGL(data, varname, test, B, which = c("score", "empirical"), min.weight = 1e-05, two.sided = TRUE, percent = 0.95)

Rd file 'probs.to.matrix.Rd':
  \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 

Rd file 'rank.genes.Rd':
  \examples lines wider than 100 characters:
     p1<-apply(Singhdata$esets[[1]],1,function(x) {t=t.test(x~Singhdata$classes[[1]], alternative="two.sided"); return(t$p.value) })
     p2<-apply(Singhdata$esets[[2]],1,function(x) {t=t.test(x~Singhdata$classes[[2]], alternative="two.sided"); return(t$p.value) })
     p3<-apply(Singhdata$esets[[3]],1,function(x) {t=t.test(x~Singhdata$classes[[3]], alternative="two.sided"); return(t$p.value) })
     T1<-apply(Singhdata$esets[[1]],1,function(x) {t=t.test(x~Singhdata$classes[[1]], alternative="two.sided"); return(t$statistic) })
     T2<-apply(Singhdata$esets[[2]],1,function(x) {t=t.test(x~Singhdata$classes[[2]], alternative="two.sided"); return(t$statistic) })
     T3<-apply(Singhdata$esets[[3]],1,function(x) {t=t.test(x~Singhdata$classes[[3]], alternative="two.sided"); return(t$statistic) })

Rd file 'selectClass.Rd':
  \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),

These lines will be truncated in the PDF manual.