diff --git a/DESCRIPTION b/DESCRIPTION index 2802d3a9..0669de47 100644 --- a/DESCRIPTION +++ b/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( diff --git a/R/ReturnPathwaysEnrich_InputAnalytes.R b/R/ReturnPathwaysEnrich_InputAnalytes.R index f3a62f88..efaca8ba 100644 --- a/R/ReturnPathwaysEnrich_InputAnalytes.R +++ b/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...") diff --git a/R/processNewRamp.R b/R/processNewRamp.R index 93b6ce8d..b9e6e8f2 100644 --- a/R/processNewRamp.R +++ b/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, diff --git a/R/sysdata.rda b/R/sysdata.rda index b5ae6b85..159f2532 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index d4675b1e..bb7fb34b 100644 --- a/README.md +++ b/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 diff --git a/inst/extdata/FT_data.Rdata b/inst/extdata/FT_data.Rdata index c4d1a2cd..c17d3d7e 100644 Binary files a/inst/extdata/FT_data.Rdata and b/inst/extdata/FT_data.Rdata differ diff --git a/inst/extdata/analytes_overlap_matrix.RData b/inst/extdata/analytes_overlap_matrix.RData index 351d2054..ec7d3389 100644 Binary files a/inst/extdata/analytes_overlap_matrix.RData and b/inst/extdata/analytes_overlap_matrix.RData differ diff --git a/inst/extdata/genes_overlap_matrix.RData b/inst/extdata/genes_overlap_matrix.RData index adcbfd17..95db4f99 100644 Binary files a/inst/extdata/genes_overlap_matrix.RData and b/inst/extdata/genes_overlap_matrix.RData differ diff --git a/inst/extdata/metabolites_overlap_matrix.RData b/inst/extdata/metabolites_overlap_matrix.RData index 788f5887..73918138 100644 Binary files a/inst/extdata/metabolites_overlap_matrix.RData and b/inst/extdata/metabolites_overlap_matrix.RData differ