Merge pull request #8 from ropensci/reddep

Reddep
ropensci · Sep 14, 2018 · 52635ea · 52635ea
2 parents 88b4923 + 25f2f21
commit 52635ea
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cRegulome
 Type: Package
-Version: 0.1.1
+Version: 0.2.0
 Title: Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
 Description: Builds a 'SQLite' database file of pre-calculated transcription 
     factor/microRNA-gene correlations (co-expression) in cancer from the 
@@ -23,24 +23,18 @@ Imports: DBI,
     RSQLite,
     UpSetR,
     VennDiagram,
-    magrittr,
-    dplyr,
     ggplot2,
     ggridges,
-    tidyr,
-    reshape2,
-    purrr,
     grid,
     R.utils,
-    AnnotationDbi,
-    org.Hs.eg.db,
-    clusterProfiler
+    igraph
 VignetteBuilder: knitr
 Suggests: knitr, 
     rmarkdown, 
     testthat,
     covr,
-    dbplyr,
-    igraph,
-    readxl
+    readxl,
+    AnnotationDbi,
+    org.Hs.eg.db,
+    clusterProfiler
 
diff --git a/NAMESPACE b/NAMESPACE
@@ -22,12 +22,24 @@ export(cor_hist)
 export(cor_igraph)
 export(cor_joy)
 export(cor_plot)
+export(cor_prep)
 export(cor_tidy)
 export(cor_upset)
 export(cor_venn_diagram)
 export(get_db)
 export(get_mir)
 export(get_tf)
-import(DBI)
-import(RSQLite)
-importFrom(magrittr,"%>%")
+export(stat_collect)
+export(stat_make)
+import(ggplot2)
+importFrom(DBI,dbListFields)
+importFrom(R.utils,gunzip)
+importFrom(RSQLite,dbGetQuery)
+importFrom(UpSetR,upset)
+importFrom(VennDiagram,venn.diagram)
+importFrom(ggridges,geom_density_ridges)
+importFrom(graphics,hist)
+importFrom(grid,grid.draw)
+importFrom(httr,http_error)
+importFrom(igraph,graph_from_data_frame)
+importFrom(utils,download.file)
diff --git a/NEWS.md b/NEWS.md
@@ -11,3 +11,8 @@
 # cRegulome 0.1.1
 
     - fix installing in default library tree
+
+# cRegulome 0.2.0
+
+    - Reduced code dependencies
+    - Improved code performance
diff --git a/R/cRegulome.R b/R/cRegulome.R
@@ -2,19 +2,36 @@
 #'
 #' Download, access and visualize Regulome (microRNA and transcription factors)
 #' data from miRCancer and Cistrome cancer
-#'
+#' 
+#' @section \code{cRegulome} functions to download and query the database file:
+#' \code{\link{get_db}}
+#' \code{\link{get_tf}}
+#' \code{\link{get_mir}}
+#' 
+#' @section \code{cRegulome} functions to create S3 objects:
+#' \code{\link{cTF}}
+#' \code{\link{cmicroRNA}}
+#' 
+#' @section \code{cRegulome} functions to reshape S3 objects:
+#' \code{\link{cor_tidy}}
+#' \code{\link{cor_igraph}}
+#' 
+#' @section \code{cRegulome} functions to visualize data in S3 objects:
+#' \code{\link{cor_hist}}
+#' \code{\link{cor_joy}}
+#' \code{\link{cor_plot}}
+#' \code{\link{cor_upset}}
+#' \code{\link{cor_venn_diagram}}
+#' 
 #' @docType package
 #' @name cRegulome
-#' 
-#' @import DBI
-#' @import RSQLite
 NULL
 
 ## quiets concerns of R CMD check re: the .'s that appear in pipelines
 ## fix by @jennybc
 ## source https://github.com/jennybc/googlesheets/blob/master/R/googlesheets.R
-if(getRversion() >= "2.15.1")  utils::globalVariables(c('study',
-                                                        'mirna_base',
-                                                        'cor',
-                                                        'tf',
-                                                        'feature'))
+#if(getRversion() >= "2.15.1")  utils::globalVariables(c('study',
+#                                                        'mirna_base',
+#                                                        'cor',
+#                                                        'tf',
+#                                                        'feature'))