Merge pull request #56 from ncats/db_rdata_update_2.3.0

commit rdata updates for DB v2.3.0, small change to method annotations

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RaMP
 Title: RaMP (Relational Database of Metabolomic Pathways)
 Type: Package
-Version: 2.3.1
+Version: 2.3.2
 License: GPL-2
 Depends: R (>= 3.6.0)
 Authors@R: c(

R/ReturnPathwaysEnrich_InputAnalytes.R

@@ -956,8 +956,7 @@ getCustomPathwayFromAnalyte <- function(analytes, pathways, analyte_type) {
 #' fisher.results <- runCombinedFisherTest(pathwaydf = pathwaydf)
 #' clustered.fisher.results <- findCluster(fisher.results)
 #' }
-#' @exportcluster_list
-
+#' @export
 findCluster <- function(fishers_df, perc_analyte_overlap = 0.5,
                         min_pathway_tocluster = 2, perc_pathway_overlap = 0.5) {
   print("Clustering pathways...")

R/processNewRamp.R

@@ -456,7 +456,7 @@ processData <- function(){
 #
 #
 #   #uncomment usethis::use_data function to create sysdata.rda object
-#   rampdb_version = 'v2.2.1'
+#   rampdb_version = 'v2.3,0'
 #   usethis::use_data(genes_result,
 #                      metabolites_result,
 #                      analyte_result,

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://api.travis-ci.com/ncats/RaMP-DB.svg?branch=custom_bg_fix2)](https://travis-ci.com/github/ncats/RaMP-DB)
+[![Build Status](https://api.travis-ci.com/ncats/RaMP-DB.svg?branch=main)](https://travis-ci.com/github/ncats/RaMP-DB)
 
 # New!  RaMP 2.0!
 
@@ -61,7 +61,7 @@ To access, [click here](https://www.mdpi.com/2218-1989/8/1/16)
 ## Installation Instructions
 In order to use this R package locally, you will need the following:
 * The R code under this repo
-* The mysql dump file that contains the RaMP database. **[Download here](https://figshare.com/ndownloader/files/39460683).**
+* The mysql dump file that contains the RaMP database. **[Download here](https://figshare.com/ndownloader/files/41731611).**
 
 
 If you would like to know how to build RaMP database from scratch, please check another GitHub site at [RaMP-BackEnd](https://github.com/ncats/RaMP-BackEnd)
@@ -89,7 +89,7 @@ mysql> exit;
 
 Here, we are naming the database "ramp" but you can use any name you'd like.  It is worth noting though that the R package assumes that the name of the database is "ramp" by default.  So if you change the name, remember to pass that name as arguments in the R package functions.
 
-Second, download and unzip the latest RaMP database. **[Download here](https://figshare.com/ndownloader/files/39460683).**
+Second, download and unzip the latest RaMP database. **[Download here](https://figshare.com/ndownloader/files/41731611).**
 
 
 Third, populate the named database with the mysql dump file