## ----设置，包括= false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(cache = TRUE) ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE--------------------库（cbioportaldata）图书馆（Anvil）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- （cbio <-cbioportal（））## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------标签（CBIO）头（标签（CBIO）$）手术） ＃＃ - - - - - - - - - - - - - - - - - - - - - - ------------------------------------------ searchOps(cbio, "clinical") ## ----------------------------------------------------------------------------- getStudies(cbio) ## ----------------------------------------------------------------------------- clinicalData(cbio, "acc_tcga") ## ----------------------------------------------------------------------------- mols <- molecularProfiles(cbio, "acc_tcga") mols[["molecularProfileId"]] ## ----------------------------------------------------------------------------- molecularData(cbio, molecularProfileId = "acc_tcga_rna_seq_v2_mrna", entrezGeneIds = c(1, 2), sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01") ) ## ----------------------------------------------------------------------------- geneTable(cbio) ## ----------------------------------------------------------------------------- genePanels(cbio) getGenePanel(cbio, "IMPACT341") ## ----------------------------------------------------------------------------- gprppa <- genePanelMolecular(cbio, molecularProfileId = "acc_tcga_rppa", sampleListId = "acc_tcga_all") gprppa ## ----------------------------------------------------------------------------- getGenePanelMolecular(cbio, molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_gistic"), sampleIds = allSamples(cbio, "acc_tcga")$sampleId ) ## ----------------------------------------------------------------------------- getDataByGenes(cbio, "acc_tcga", genePanelId = "IMPACT341", molecularProfileId = "acc_tcga_rppa", sampleListId = "acc_tcga_rppa") ## ----------------------------------------------------------------------------- sampleLists(cbio, "acc_tcga") ## ----------------------------------------------------------------------------- samplesInSampleLists(cbio, "acc_tcga_cna") ## ----------------------------------------------------------------------------- samplesInSampleLists(cbio, c("acc_tcga_cna", "acc_tcga_cnaseq")) ## ----------------------------------------------------------------------------- allSamples(cbio, "acc_tcga") ## ----------------------------------------------------------------------------- getSampleInfo(cbio, studyId = "acc_tcga", sampleListIds = c("acc_tcga_rppa", "acc_tcga_gistic")) ## ----------------------------------------------------------------------------- cbio$getGeneUsingGET ## ----------------------------------------------------------------------------- (resp <- cbio$getGeneUsingGET("BRCA1")) ## ----------------------------------------------------------------------------- httr::content(resp) ## ----eval=FALSE--------------------------------------------------------------- # unlink("~/.cache/cBioPortalData/") ## ----------------------------------------------------------------------------- sessionInfo()