[GDR-3409] Add prism data - first phase by j-smola · Pull Request #78 · gdrplatform/gDRtestData

j-smola · 2026-06-02T12:00:21Z

Description

What changed?

Related JIRA issue: GDR-3409

Why was it changed?

To allow using PRISM data in examples accross gDRplatform

Checklist for sustainable code base

I added tests for any code changed/added
I added documentation for any code changed/added
I made sure naming of any new functions is self-explanatory and consistent

Logistic checklist

Package version bumped
Changelog updated

Screenshots (optional)

gemini-code-assist

Code Review

This pull request updates the gDRtestData package to version 1.11.4, introducing the PRISM public dataset and expanding the documentation for several DepMap datasets by adding loading instructions, detailed descriptions, and updating keywords to 'real_data'. The review feedback identifies minor grammatical typos in the documentation and generated .Rd files, specifically recommending the pluralization of 'genes as columns' and '774 cell lines'.

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gemini-code-assist · 2026-06-02T12:01:19Z

+#' package = "gDRtestData"))}
 #'
-#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#' @format Matrix with cell lines as rows and genes as column


There is a grammatical typo in the @format description. 'genes as column' should be pluralized to 'genes as columns'.

#' @format Matrix with cell lines as rows and genes as columns

gemini-code-assist · 2026-06-02T12:01:19Z

+#' PRISM Broad Screen Cancer Cell Line Viability Dataset
+#'
+#' The single-agent screening data from the PRISM platform -
+#' with one drug and 774 cell line.


There is a grammatical typo in the description. '774 cell line' should be pluralized to '774 cell lines'.

#' with one drug and 774 cell lines.

gemini-code-assist · 2026-06-02T12:01:19Z

-}
-\source{
-\url{https://depmap.org/portal/data_page/?tab=allData}
+Matrix with cell lines as rows and genes as column


There is a grammatical typo in the \format section. 'genes as column' should be pluralized to 'genes as columns'.

Matrix with cell lines as rows and genes as columns

gemini-code-assist · 2026-06-02T12:01:19Z

+}
+\description{
+The single-agent screening data from the PRISM platform -
+with one drug and 774 cell line.


There is a grammatical typo in the description. '774 cell line' should be pluralized to '774 cell lines'.

with one drug and 774 cell lines.

gladkia

GJ!

bczech · 2026-06-02T14:10:54Z

+#' @section Description:
+#' - Rows: Cell line identifiers
+#' - Columns: Metadata columns (see below)
+#' - Values: Cell line annotations and patient information


There are no patients, these are in vitro data. These are donors

Suggested change

#' - Values: Cell line annotations and patient information

#' - Values: Cell line annotations and donor demographics

bczech · 2026-06-02T14:15:54Z

-| **Rows** | Individual cell lines (~1,000 models) |
+| **Rows** | Individual cell lines |
 | **Columns** | Metadata columns (see below) |
 | **Values** | Cell line annotations and patient information |


bczech · 2026-06-02T14:16:19Z

+#'   \item{clid}{Unique Broad Institute cell line identifier.}
+#'   \item{CellLineName}{Publicly recognized cancer cell line name.}
+#'   \item{Tissue}{Primary tissue of origin.}
+#'   \item{parental_identifier}{Identifier for parental strain/patient source.}


Not patient source — it's a parental cell line identifier.

Suggested change

#' \item{parental_identifier}{Identifier for parental strain/patient source.}

#' \item{parental_identifier}{Identifier for the parental cell line.}

bczech · 2026-06-02T14:16:22Z

+#' ### Row Metadata (rowData)
+#' Feature metadata describing the treatment compounds across assays:
+#' \describe{
+#'   \item{Gnumber}{Broad Institute global substance identifier (Genentech/Broad ID).}


Gnumber is a Genentech identifier, not Broad Institute.

Suggested change

#' \item{Gnumber}{Broad Institute global substance identifier (Genentech/Broad ID).}

#' \item{Gnumber}{Genentech compound identifier.}

j-smola added 5 commits June 2, 2026 09:52

chore: update data description

d44787d

doc: update data description

0f1fc0f

doc: update data description

82fec3b

chore: add prism data

d6290b1

doc: add prism data

1e4194b

j-smola requested review from bczech, darsoo and gladkia June 2, 2026 12:00

j-smola requested a review from a team as a code owner June 2, 2026 12:00

gemini-code-assist Bot reviewed Jun 2, 2026

View reviewed changes

chore: as per review

35067f9

gladkia approved these changes Jun 2, 2026

View reviewed changes

darsoo approved these changes Jun 2, 2026

View reviewed changes

bczech reviewed Jun 2, 2026

View reviewed changes

	#' - Values: Cell line annotations and patient information
	#' - Values: Cell line annotations and donor demographics

	\| Values \| Cell line annotations and patient information \|
	\| Values \| Cell line annotations and metadata \|

	#' \item{parental_identifier}{Identifier for parental strain/patient source.}
	#' \item{parental_identifier}{Identifier for the parental cell line.}

	#' \item{Gnumber}{Broad Institute global substance identifier (Genentech/Broad ID).}
	#' \item{Gnumber}{Genentech compound identifier.}

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j-smola commented Jun 2, 2026

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