Update documentation (no major changes)

shbrief · Jul 26, 2022 · d33811f · d33811f
1 parent 52a5bdb
commit d33811f
Show file tree

Hide file tree

Showing 16 changed files with 40 additions and 350 deletions.
diff --git a/R/PCAGenomicSignatures-methods.R b/R/PCAGenomicSignatures-methods.R
@@ -12,6 +12,8 @@
 #' @param ... Additional arguments for supporting functions.
 #'
 #' @return a character vector
+#' 
+#' @keywords internal
 #'
 .RAVName <- function(x, ...) {
     rownames(x@colData) <- paste0("RAV", seq_len(ncol(x)))

diff --git a/R/buildAvgLoading.R b/R/buildAvgLoading.R
@@ -10,6 +10,8 @@
 #' @param kmeansRes Output from \code{stats::kmeans}.
 #'
 #' @return Silhouette-class object, which is an n x 3 matrix with attributes.
+#' 
+#' @keywords internal
 #'
 #' @seealso \code{\link[stats]{kmeans}}
 #'

diff --git a/R/data.R b/R/data.R
@@ -19,7 +19,7 @@
 
 
 #' @name filterList
-#' @title RAVs that will output with quanlity-control messages
+#' @title RAVs that will output with quality-control messages
 #' @format A named list with four elements - "Cluster_Size_filter",
 #' "GSEA_C2_filter", "GSEA_PLIERpriors_filter", and "Redundancy_filter".
 #' @author Sehyun Oh \email{[email protected]}

diff --git a/R/funcForGSEA.R b/R/funcForGSEA.R
diff --git a/R/plotAnnotatedPCA.R b/R/plotAnnotatedPCA.R
@@ -2,7 +2,6 @@
 #'
 #' @import ggpubr
 #' @import ggplot2
-#' @import flextable
 #'
 #' @param dataset A gene expression profile to be validated. Different classes
 #' of objects can be used including ExpressionSet, SummarizedExperiment,

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -50,6 +50,15 @@ reference:
       - plotAnnotatedPCA
       - plotValidate
       - sampleScoreHeatmap
+  - title: Misc. Package Docs
+    desc: Other package information and data
+    contents:
+      - droplist
+      - filterList
+      - miniAllZ
+      - miniRAVmodel
+      - miniTCGA
+      - res_hcut
 
 navbar:
   title: ~

diff --git a/man/dot-RAVName.Rd b/man/dot-RAVName.Rd
diff --git a/man/dot-calculateSilhouetteWidth.Rd b/man/dot-calculateSilhouetteWidth.Rd
diff --git a/man/dot-loadingCor.Rd b/man/dot-loadingCor.Rd
diff --git a/man/filterList.Rd b/man/filterList.Rd
diff --git a/man/makeGeneList.Rd b/man/makeGeneList.Rd
diff --git a/man/msigdb_gsea.Rd b/man/msigdb_gsea.Rd
diff --git a/man/plotAnnotatedPCA.Rd b/man/plotAnnotatedPCA.Rd