inst/scripts/README.md

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

The .csv files in this package originate from the Broad Institute Depmap Data Portal: https://depmap.org/portal/download/

These datafiles have been put in long format via dplyr for usage with R packages such as ggplot2. The only modification of the datasets is that the datasets have been renamed to shorter names (such as "metadata") and the column names have been changed to snake case. The data has been put on ExperimentHub AWS for easy access and to keep this package lightweight.

If the need arises to reproduce the data files manually, they can be generated by running the make-data.R scripts (of the appropriate version) found in this directory. In order to generate the .rda data files correctly, it is necessary to create an empty directory ./inst/eh_data to generate the data per the make-data.R scripts.

In this directory, save ./inst/scripts/data.R that load the csv files and save the rda files directly in ./data/.

## example
ccle_depmap <- read.csv("../extdata/CCLE_depMap_19Q1_TPM.zip")
## cleaning, ...
save(ccle_depmap, file = "../../data/ccle_depmap.rda", 
     compress = "xz", compression_level = 9)

UCLouvain-CBIO/depmap documentation built on Aug. 18, 2024, 9:46 p.m.