## ----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()