@@ -10,8 +10,8 @@

 #' @export

 #'

 #' @examples

-#' library(airway)

-#' data(airway)

+#' library("airway")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

 #'                                              colData = colData(airway),

@@ -60,8 +60,8 @@ To obtain a list, type mart = useMart('ensembl'), followed by listDatasets(mart)

 #' @export

 #'

 #' @examples

-#' library(airway)

-#' data(airway)

+#' library("airway")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

 #'                                              colData = colData(airway),

@@ -12,8 +12,8 @@

 #' @export

 #'

 #' @examples

-#' library(airway)

-#' data(airway)

+#' library("airway")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

 #'                                              colData = colData(airway),

@@ -33,9 +33,9 @@

 #' @return A table containing the computed GO Terms and related enrichment scores

 #'

 #' @examples

-#' library(airway)

-#' library(DESeq2)

-#' data(airway)

+#' library("airway")

+#' library("DESeq2")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)

 #' # Example, performing extraction of enriched functional categories in

@@ -145,9 +145,9 @@ topGOtable <- function(DEgenes,                  # Differentially expressed gene

 #' of the main [pcaExplorer()] function

 #'

 #' @examples

-#' library(airway)

-#' library(DESeq2)

-#' data(airway)

+#' library("airway")

+#' library("DESeq2")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)

 #' \dontrun{

@@ -310,10 +310,10 @@ rankedGeneLoadings <- function(x, pc = 1, decreasing = TRUE) {

 #' of the main [pcaExplorer()] function

 #'

 #' @examples

-#' library(airway)

-#' library(DESeq2)

-#' library(limma)

-#' data(airway)

+#' library("airway")

+#' library("DESeq2")

+#' library("limma")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)

 #' \dontrun{

@@ -25,8 +25,8 @@

 #' @return A Shiny App is launched for interactive data exploration

 #'

 #' @examples

-#' library(airway)

-#' data(airway)

+#' library("airway")

+#' data("airway", package = "airway")

 #' airway

 #' dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

 #'                                              colData = colData(airway),

@@ -279,9 +279,9 @@ count quantifications can be found in the `airway` package vignette.

 To run `pcaExplorer` on this dataset, the following commands are required

 ```

-library(airway)

+library("airway"")

-data(airway)

+data("airway", package = "airway")

 dds_airway <- DESeqDataSet(airway,design=~dex+cell)

 dds_airway

@@ -293,7 +293,7 @@ pcaExplorer(dds = dds_airway,

 The `annotation` for this dataset can be built by exploiting the `org.Hs.eg.db` package

 ```

-library(org.Hs.eg.db)

+library("org.Hs.eg.db")

 genenames_airway <- mapIds(org.Hs.eg.db,keys = rownames(dds_airway),column = "SYMBOL",keytype="ENSEMBL")

 annotation_airway <- data.frame(gene_name = genenames_airway,

                                 row.names = rownames(dds_airway),

@@ -22,8 +22,8 @@ A data frame for ready use in \code{pcaExplorer}, retrieved from biomaRt.

 Get an annotation data frame from biomaRt

 }

 \examples{

-library(airway)

-data(airway)

+library("airway")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

                                              colData = colData(airway),

@@ -29,8 +29,8 @@ org db packages

 Get an annotation data frame from org db packages

 }

 \examples{

-library(airway)

-data(airway)

+library("airway")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

                                              colData = colData(airway),

@@ -48,10 +48,10 @@ performs functional enrichment analysis on them using the simple and quick routi

 provided by the \code{limma} package

 }

 \examples{

-library(airway)

-library(DESeq2)

-library(limma)

-data(airway)

+library("airway")

+library("DESeq2")

+library("limma")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)

 \dontrun{

@@ -25,8 +25,8 @@ A plot with pairwise scatter plots and correlation coefficients

 Pairwise scatter and correlation plot of counts

 }

 \examples{

-library(airway)

-data(airway)

+library("airway")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

                                              colData = colData(airway),

@@ -62,9 +62,9 @@ performs functional enrichment analysis on them using routines and algorithms fr

 the \code{topGO} package

 }

 \examples{

-library(airway)

-library(DESeq2)

-data(airway)

+library("airway")

+library("DESeq2")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)

 \dontrun{

@@ -48,8 +48,8 @@ Launch a Shiny App for interactive exploration of a dataset from the perspective

 of Principal Components Analysis

 }

 \examples{

-library(airway)

-data(airway)

+library("airway")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),

                                              colData = colData(airway),

@@ -71,9 +71,9 @@ following: \code{elim}, \code{weight}, \code{weight01}, \code{lea},

 documentation of the \code{topGO} package itself

 }

 \examples{

-library(airway)

-library(DESeq2)

-data(airway)

+library("airway")

+library("DESeq2")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)

 # Example, performing extraction of enriched functional categories in

@@ -3,9 +3,9 @@ library(pcaExplorer)

 context("Checks on the functional enrichment of subset of genes/genes with hi loadings")

 # testing this is quite lengthy... explore other possibilities?

-library(airway)

-library(DESeq2)

-data(airway)

+library("airway")

+library("DESeq2")

+data("airway", package = "airway")

 airway

 dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)

@@ -384,10 +384,10 @@ Otherwise, to run `r Biocpkg("pcaExplorer")` on this dataset from the terminal/R

 First, prepare the objects to be passed as parameters of `r Biocpkg("pcaExplorer")`.

 ```{r loadairway, message=FALSE}

-library(airway)

-library(DESeq2)

+library("airway")

+library("DESeq2")

-data(airway)

+data("airway", package = "airway")

 dds_airway <- DESeqDataSet(airway,design= ~ cell + dex)

 dds_airway