## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----echo = FALSE------------------------------------------------------------- suppressPackageStartupMessages(library("tidyverse")) ## ----install, eval=FALSE------------------------------------------------------ # install.packages("BiocManager") # BiocManager::install("depmap") ## ----import_EH, message = FALSE----------------------------------------------- library("depmap") library("ExperimentHub") ## ----ehquery------------------------------------------------------------------ ## create ExperimentHub query object eh <- ExperimentHub() query(eh, "depmap") ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2260"]] ## ----------------------------------------------------------------------------- depmap::depmap_rnai() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2261"]] ## ----------------------------------------------------------------------------- depmap::depmap_crispr() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2262"]] ## ----------------------------------------------------------------------------- depmap::depmap_copyNumber() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2263"]] ## ----------------------------------------------------------------------------- depmap::depmap_RPPA() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2264"]] ## ----------------------------------------------------------------------------- depmap::depmap_TPM() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2266"]] ## ----------------------------------------------------------------------------- depmap::depmap_metadata() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH2265"]] ## ----------------------------------------------------------------------------- depmap::depmap_mutationCalls() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH3087"]] ## ----------------------------------------------------------------------------- depmap::depmap_drug_sensitivity() ## ----eval = FALSE------------------------------------------------------------- # eh[["EH3459"]] ## ----------------------------------------------------------------------------- depmap::depmap_proteomic() ## ----------------------------------------------------------------------------- dmsets() ## ----message=FALSE------------------------------------------------------------ library(tidyverse) dmsets() |> filter(grepl("20Q", title)) ## ----------------------------------------------------------------------------- dmfiles() ## ----------------------------------------------------------------------------- dmfiles() |> filter(dataset_id == 20564034) ## ----------------------------------------------------------------------------- dmfiles() |> filter(name == "prism-repurposing-20q2-primary-screen-cell-line-info.csv") |> dmget() ## ----------------------------------------------------------------------------- dmfiles() |> filter(name == "prism-repurposing-20q2-primary-screen-cell-line-info.csv") |> dmget() |> read_csv() ## ----------------------------------------------------------------------------- ids_2020 <- filter(dmsets(), grepl("20Q", title)) |> pull(dataset_id) dmfiles() |> filter(dataset_id %in% ids_2020) |> filter(grepl("README", name)) |> dmget() ## ----echo = FALSE------------------------------------------------------------- sessionInfo()