Merge pull request #96 from apeltzer/master

Adding Depmap 24Q2 data to dmsets()

DESCRIPTION

@@ -6,8 +6,10 @@ Authors@R: c(person(given = "Laurent", family = "Gatto",
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0002-1520-2268"),
                     role = c("cre", "aut")),
-             person(given = "Theo", family = "Killian",
-                    role = "aut"))
+            person(given = "Theo", family = "Killian",
+                    role = "aut"),
+            person(given = "Alexander", family = "Peltzer", role = "aut",
+                    comment = c(ORCID = "0000-0002-6503-2180")))
 Description: The depmap package is a data package that accesses datsets from the
     Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets
     from the most current release are available, including RNAI and CRISPR-Cas9

NEWS.md

@@ -1,5 +1,9 @@
 # depmap 1.19
 
+## Changes in version 1.19.1
+
+- Added 24Q2 data to `dmsets` and `dmfiles` to enable latest data to be analyzed
+
 ## Changes in version 1.19.0
 
 - New devel version.

inst/scripts/make-dmfiles.R

@@ -1,8 +1,9 @@
 ## List of URLs obtained from the DepMap Figshare page
 ## (https://figshare.com/authors/Broad_DepMap/5514062) on the
-## 25 February 2024.
+## 15 August 2024
 depmapURLs <-
-    c("https://figshare.com/articles/dataset/DepMap_23Q4_Public/24667905",
+    c("https://figshare.com/articles/dataset/DepMap_24Q2_Public/25880521",
+      "https://figshare.com/articles/dataset/DepMap_23Q4_Public/24667905",
       "https://figshare.com/articles/dataset/DepMap_23Q2_Public/22765112",
       "https://figshare.com/articles/dataset/DepMap_22Q4_Public/21637199",
       "https://figshare.com/articles/dataset/DepMap_22Q2_Public/19700056",
@@ -39,7 +40,6 @@ dmsets <- tibble(url = depmapURLs) |>
 dmfiles <- DepMapFiles(dmsets$data)
 ## or dmfiles <- DepMapFiles(DepMapDataset(depmap$dataset_id))
 
-
-extdata <- "~/wrk/depmap/inst/extdata"
+extdata <- "~/repos/OS/depmap/inst/extdata"
 saveRDS(dmsets, file = file.path(extdata, "dmsets.rds"))
 saveRDS(dmfiles, file = file.path(extdata, "dmfiles.rds"))