minimal cleaning; working version before major changes

Aclust.Rproj

@@ -15,3 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran

R/Acluster.R

@@ -29,7 +29,9 @@ function(ordr.vec, thresh.dist, which.clust = NULL, location.vec = NULL, max.dis
 				clust.2.min <- k +1
 				clust.2.max <- last(which.clust[which.clust == which.clust[k + 1]])
 
-				dist.clust[k] <- calc.dist.clusters(ordr.vec[,clust.1.min:clust.1.max], ordr.vec[,clust.2.min:clust.2.max], type = type, dist.type = dist.type)
+				dist.clust[k] <- calc.dist.clusters(ordr.vec[,clust.1.min:clust.1.max], 
+                                            ordr.vec[,clust.2.min:clust.2.max], 
+                                            type = type, dist.type = dist.type)
 
 				}
 		}

R/annot.clusters.R

@@ -4,7 +4,7 @@ function(clusters.list, annot = NULL, annotation.file.name = NULL, required.anno
 
 	if (is.null(annot)) {
 		if (!is.null(annotation.file.name)){
-			cat("Loading annotation from Illumina's menifest", "\n")
+			cat("Loading annotation from Illumina's manifest", "\n")
 			annot <- read.csv(annotation.file.name, skip = 7)
 			annot <- data.table(annot)
 			setkeyv(annot, c("CHR","Coordinate_36") ) } else{

R/annot.probe.vec.R

@@ -5,7 +5,7 @@ function(probe.vec, annot = NULL, annotation.file.name = NULL, required.annotati
 
   if (is.null(annot)) {
 		if (!is.null(annotation.file.name)){
-			cat("Loading annotation from Illumina's menifest", "\n")
+			cat("Loading annotation from Illumina's manifest", "\n")
 			annot <- read.csv(annotation.file.name, skip = 7)
 			annot <- data.table(annot)
 			setkeyv(annot, c("CHR","Coordinate_36") ) } else{

man/load.annotation.Rd

@@ -23,7 +23,7 @@ A data.table object with the annotation.
 \examples{
 
 ### not run! need to put the appropriate path to the annotation file
-# annotation.file.name <- "illumina_450_menifest_v.1.2.csv"
+# annotation.file.name <- "illumina_450_manifest_v.1.2.csv"
 # annot <- load.annotation(annotation.file.name)
 # annot[1:5]
 }

man/summarize.top.clusters.Rd

@@ -43,7 +43,7 @@ A significance p-value threshold (after FDR correction). Only clusters with p-va
 An effect size threshold. Only clusters with estimated effect size larger than cutoff.effect.size will be reported. 
 }
   \item{annot}{
-annotation data table. The package uses the Illumina annotation file ``illumina_450_menifest_v.1.2". 
+annotation data table. The package uses the Illumina annotation file ``illumina_450_manifest_v.1.2". 
 }
   \item{annotation.file.name}{
 A name of annotation file to read. By default it is not required, since one can use `annot', which is in the package.