## ----设置，包括= FALSE ---------------------------------------------------- knitr: opts_chunk设置(缓存= TRUE) # #美元——包括= TRUE,结果=“隐藏”,消息= FALSE,警告= FALSE ------------------ 库(cBioPortalData)库(铁砧 ) ## ----------------------------------------------------------------------------- ( cbio < - cBioPortal ()) ## ----------------------------------------------------------------------------- 标记(cbio)头(标签(cbio)操作美元)# #----------------------------------------------------------------------------- 临床searchOps (cbio。 ") ## ----------------------------------------------------------------------------- getStudies (cbio ) ## ----------------------------------------------------------------------------- acc_tcga clinicalData (cbio。 ") ## ----------------------------------------------------------------------------- 摩尔< - molecularProfiles (cbio“acc_tcga”)摩尔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美元 ) ## ----------------------------------------------------------------------------- getDataByGenes (cbio“acc_tcga genePanelId =“IMPACT341 molecularProfileId =“acc_tcga_rppa sampleListId = " acc_tcga_rppa ") ## ----------------------------------------------------------------------------- acc_tcga sampleLists (cbio。 ") ## ----------------------------------------------------------------------------- samplesInSampleLists (cbio“acc_tcga_cna ") ## ----------------------------------------------------------------------------- samplesInSampleLists (cbio c(“acc_tcga_cna”、“acc_tcga_cnaseq ")) ## ----------------------------------------------------------------------------- acc_tcga allSamples (cbio。 ") ## ----------------------------------------------------------------------------- getSampleInfo (cbio studyId =“acc_tcga sampleListIds = c(“acc_tcga_rppa”,“acc_tcga_gistic ")) ## ----------------------------------------------------------------------------- cbio getGeneUsingGET美元 ## ----------------------------------------------------------------------------- ( resp < - cbio getGeneUsingGET美元(“BRCA1 ")) ## ----------------------------------------------------------------------------- httr:内容(职责)# # - eval = FALSE --------------------------------------------------------------- # 分离(~ / .cache / cBioPortalData) # #----------------------------------------------------------------------------- sessionInfo ()