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Adding Depmap 24Q2 data to dmsets() #96

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merged 5 commits into from
Aug 15, 2024
Merged

Adding Depmap 24Q2 data to dmsets() #96

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8c0f6aa
Update to include DepMap 24Q2 too
apeltzer Aug 15, 2024
c8aeb41
Consistent URL
apeltzer Aug 15, 2024
254dbf3
Added dmfiles and dmsets with 24Q2 data
apeltzer Aug 15, 2024
9a44b33
Add description and news
apeltzer Aug 15, 2024
fe32331
Resolve merge conflict, make 1.19.1
apeltzer Aug 15, 2024
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6 changes: 4 additions & 2 deletions DESCRIPTION
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Expand Up @@ -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
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -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.
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8 changes: 4 additions & 4 deletions inst/scripts/make-dmfiles.R
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@@ -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",
Expand Down Expand Up @@ -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"))