updated biocviews to fix dependency issue and use BiocFileCache

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: leapR
 Title: Layered enrichment analysis of pathways R
-Version: 0.99.8
+Version: 0.99.9
 Authors@R: c(
     person("Sara", "Gosline", email = "sara.gosline@pnnl.gov", role = c('aut',"cre"), comment = c(ORCID = "0000-0002-6534-4774")),
     person("Jason", "McDermott", email = "jason.mcdermott@pnnl.gov", role = "aut"),
@@ -17,7 +17,8 @@ biocViews:
   Proteomics,
   Pathways,
   GeneExpression, 
-  Transcriptomics
+  Transcriptomics,
+  Software
 Imports:
     stats,
     gplots,
@@ -30,11 +31,13 @@ Imports:
     stringr,
     tidyr,
     SummarizedExperiment, 
-    BiocStyle
+    BiocStyle,
+    BiocFileCache
 Suggests: 
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 License: MIT + file LICENSE
 Config/testthat/edition: 3
+URL: https://pnnl.github.io/leapR/

R/calcTTest.R

@@ -18,11 +18,15 @@
 #' @examples
 #'
 #'         library(leapR)
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
-#'
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
+#'         
 #'         # read in the pathways
 #'         data("ncipid")
 #'

R/cluster_enrichment.R

@@ -19,12 +19,14 @@
 #' @export
 #' @examples
 #'         library(leapR)
-#'
-#'         # read in the example transcriptomic data
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'
 #'         # read in the pathways
 #'         data("ncipid")

R/combine_omics.R

@@ -18,23 +18,21 @@
 #'
 #' @examples
 #'         library(leapR)
-#'         url <- 'https://api.figshare.com/v2/file/download/56536217'
-#'
-#'         pdata <- download.file(url,method='libcurl',destfile='protData.rda')
-#'         load('protData.rda')
-#'         p <- file.remove("protData.rda")
-#'
+#'         library(BiocFileCache)
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536217"
+#'         pc <- bfcadd(bfc, "pdat", fpath = url)
+#'         load(pc)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
-#'
-#'         url <- 'https://api.figshare.com/v2/file/download/56536211'
-#'         phdata<-download.file(url,method='libcurl',destfile = 'phosData.rda')
-#'         #phosphodata<-read.csv("phdata",check.names=FALSE,row.names=1)
-#'         load('phosData.rda')
-#'         p <- file.remove('phosData.rda')# read in the example protein data
-#'
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536211"
+#'         phc <- bfcadd(bfc, "phdat", fpath = url)
+#'         load(phc)
 #'
 #'         # merge the three datasets by rows and add prefix tags for
 #'         # different omics types

R/enrichment_in_groups.R

@@ -18,6 +18,7 @@
 #' to log your data before calling. NOTE: if you do not call `suppressWarnings` then
 #' the KS test will warn you about ties.
 #' @param minsize minimum size of set
+#' @param log_transformed Set to TRUE if data is already log-transformed
 #' @param mapping_column column name of mapping identifiers
 #' @param abundance_column columns mapping abundance, either in the `assay`
 #' matrix or `rowData`
@@ -114,7 +115,7 @@ enrichment_in_groups <- function(geneset,
       names(backvals) <- backlist#[-group_ind]
       in_back <- length(backvals)
 
-      outgroup_mean = mean(backvals[-group_ind], na.rm = T)
+      outgroup_mean = mean(backvals[-group_ind], na.rm = TRUE)
 
       in_path <- length(in_group) #how many left after na.rm
       if ((in_path > minsize) & (any(!is.na(in_path))) &

R/leapR-package.R

@@ -143,14 +143,14 @@
 #' \cr
 #' @examples
 #'         library(leapR)
-#'
-#'  # read in the example abundance data
-#'  # read in the example transcriptomic data
-#'  tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",
-#'       method='libcurl',destfile='transData.rda')
-#'  load('transData.rda')
-#'  p <- file.remove("transData.rda")
-#'
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536214"
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'  # read in the pathways
 #'  data("ncipid")
 #'

R/leapR.R

@@ -140,13 +140,14 @@
 #' \cr
 #' @examples
 #'         library(leapR)
-#'
-#'  # read in the example abundance data
-#'  # read in the example transcriptomic data
-#'  tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",
-#'       method='libcurl',destfile='transData.rda')
-#'  load('transData.rda')
-#'  p <- file.remove("transData.rda")
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536214"
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'
 #'  # read in the pathways
 #'  data("ncipid")

leapR.Rproj

@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

vignettes/examples.Rmd

@@ -31,6 +31,7 @@ library(ggplot2)
 library(dplyr)
 library(tibble)
 library(stringr)
+library(BiocFileCache)
 ```
 
 #  Example data
@@ -44,22 +45,23 @@ as example.
 
 This data can be loaded as follows:
 ```{r omicsdata, message=FALSE, warning=FALSE}
-url <- "https://api.figshare.com/v2/file/download/56536217"
-pdata <- download.file(url, method = "libcurl", destfile = "protData.rda")
-#  as.matrix()
-load("protData.rda")
 
-p <- file.remove("protData.rda")
+#currently using the BiocFileCache though i'm not sure it helps
+path <- tools::R_user_dir("leapR", which = "cache")
+bfc <- BiocFileCache(path, ask = FALSE)
+
+url <- "https://api.figshare.com/v2/file/download/56536217"
+pc <- bfcadd(bfc, "pdat", fpath = url)
+load(pc)
 
 url <- "https://api.figshare.com/v2/file/download/56536214"
-tdata <- download.file(url, method = "libcurl", destfile = "transData.rda")
-load("transData.rda")
-p <- file.remove("transData.rda")
+tc <- bfcadd(bfc, "tdat", fpath = url)
+load(tc)
 
 url <- "https://api.figshare.com/v2/file/download/56536211"
-phdata <- download.file(url, method = "libcurl", destfile = "phosData.rda")
-load("phosData.rda")
-p <- file.remove("phosData.rda")
+phc <- bfcadd(bfc, "phdat", fpath = url)
+load(phc)
+
 ```
 
 We also have local data we can load