## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----echo = FALSE------------------------------------------------------------- suppressPackageStartupMessages(library("dplyr")) ## ----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") ## ----echo = FALSE------------------------------------------------------------- rnai <- eh[["EH2260"]] ## ----eval = FALSE------------------------------------------------------------- # rnai <- eh[["EH2260"]] ## ----------------------------------------------------------------------------- rnai ## ----------------------------------------------------------------------------- depmap::depmap_rnai() ## ----echo = FALSE------------------------------------------------------------- rm(rnai) ## ----echo = FALSE------------------------------------------------------------- crispr <- eh[["EH2261"]] ## ----eval = FALSE------------------------------------------------------------- # crispr <- eh[["EH2261"]] ## ----------------------------------------------------------------------------- crispr ## ----------------------------------------------------------------------------- depmap::depmap_crispr() ## ----echo = FALSE------------------------------------------------------------- rm(crispr) ## ----echo = FALSE------------------------------------------------------------- copyNumber <- eh[["EH2262"]] ## ----eval = FALSE------------------------------------------------------------- # copyNumber <- eh[["EH2262"]] ## ----------------------------------------------------------------------------- copyNumber ## ----------------------------------------------------------------------------- depmap::depmap_copyNumber() ## ----echo = FALSE------------------------------------------------------------- rm(copyNumber) ## ----echo = FALSE------------------------------------------------------------- RPPA <- eh[["EH2263"]] ## ----eval = FALSE------------------------------------------------------------- # RPPA <- eh[["EH2263"]] ## ----------------------------------------------------------------------------- RPPA ## ----------------------------------------------------------------------------- depmap::depmap_RPPA() ## ----echo = FALSE------------------------------------------------------------- rm(RPPA) ## ----echo = FALSE------------------------------------------------------------- TPM <- eh[["EH2264"]] ## ----eval = FALSE------------------------------------------------------------- # TPM <- eh[["EH2264"]] ## ----------------------------------------------------------------------------- TPM ## ----------------------------------------------------------------------------- depmap::depmap_TPM() ## ----echo = FALSE------------------------------------------------------------- rm(TPM) ## ----echo = FALSE------------------------------------------------------------- metadata <- eh[["EH2266"]] ## ----eval = FALSE------------------------------------------------------------- # metadata <- eh[["EH2266"]] ## ----------------------------------------------------------------------------- metadata ## ----------------------------------------------------------------------------- depmap::depmap_metadata() ## ----echo = FALSE------------------------------------------------------------- rm(metadata) ## ----echo = FALSE------------------------------------------------------------- mutationCalls <- eh[["EH2265"]] ## ----eval = FALSE------------------------------------------------------------- # mutationCalls <- eh[["EH2265"]] ## ----------------------------------------------------------------------------- mutationCalls ## ----------------------------------------------------------------------------- depmap::depmap_mutationCalls() ## ----echo = FALSE------------------------------------------------------------- rm(mutationCalls) ## ----echo = FALSE------------------------------------------------------------- drug_sensitivity <- eh[["EH3087"]] ## ----eval = FALSE------------------------------------------------------------- # drug_sensitivity <- eh[["EH3087"]] ## ----------------------------------------------------------------------------- drug_sensitivity ## ----------------------------------------------------------------------------- depmap::depmap_drug_sensitivity() ## ----echo = FALSE------------------------------------------------------------- rm(drug_sensitivity) ## ----echo = FALSE------------------------------------------------------------- proteomic <- eh[["EH3459"]] ## ----eval = FALSE------------------------------------------------------------- # proteomic <- eh[["EH3459"]] ## ----------------------------------------------------------------------------- proteomic ## ----------------------------------------------------------------------------- depmap::depmap_proteomic() ## ----echo = FALSE------------------------------------------------------------- rm(proteomic) ## ----echo = FALSE------------------------------------------------------------- sessionInfo()