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library(devtools) #install_github("cBioPortal/cgdsr") library("cgdsr") mycgds = CGDS("http://www.cbioportal.org/") test(mycgds) # 查看肿瘤相关研究 (mycancerstuy = getCancerStudies(mycgds)[,c(1,2)]) #cancer_study_id name #1 paac_jhu_2014 Acinar Cell Carcinoma of the Pancreas (JHU, J Pathol 2014) #2 mel_tsam_liang_2017 Acral Melanoma (TGEN, Genome Res 2017) (mycancerstudy = getCancerStudies(mycgds)[106,1]) # gbm_tcga (mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[,c(1,2)]) #genetic_profile_id genetic_profile_name #1 gbm_tcga_rppa Protein expression (RPPA) #2 gbm_tcga_rppa_Zscores Protein expression z-scores (RPPA) #3 gbm_tcga_gistic Putative copy-number alterations from GISTIC #4 gbm_tcga_mrna_U133 mRNA expression (U133 microarray only) #5 gbm_tcga_mrna_U133_Zscores mRNA expression z-scores relative to diploid samples (U133 microarray only) #6 gbm_tcga_mrna mRNA expression (microarray) #7 gbm_tcga_mrna_median_Zscores mRNA expression z-scores relative to diploid samples (microarray) #8 gbm_tcga_rna_seq_v2_mrna mRNA expression (RNA Seq V2 RSEM) #9 gbm_tcga_rna_seq_v2_mrna_median_Zscores mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM) #10 gbm_tcga_linear_CNA Capped relative linear copy-number values #11 gbm_tcga_methylation_hm27 Methylation (HM27) #12 gbm_tcga_methylation_hm450 Methylation (HM450) #13 gbm_tcga_mutations Mutations #14 gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM) #15 gbm_tcga_mrna_median_all_sample_Zscores mRNA expression z-scores relative to all samples (log microarray) #16 gbm_tcga_mrna_U133_all_sample_Zscores mRNA expression z-scores relative to all samples (U133 microarray only) (mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[3,1]) # gbm_tcga_gistic (mycaselist = getCaseLists(mycgds,mycancerstudy)[,c(1,2)]) #case_list_id case_list_name #1 gbm_tcga_all All samples #2 gbm_tcga_3way_complete Complete samples #3 gbm_tcga_cna Samples with CNA data #4 gbm_tcga_methylation_all Samples with methylation data #5 gbm_tcga_methylation_hm27 Samples with methylation data (HM27) #6 gbm_tcga_methylation_hm450 Samples with methylation data (HM450) #7 gbm_tcga_mrna Samples with mRNA data (Agilent microarray) #8 gbm_tcga_rna_seq_v2_mrna Samples with mRNA data (RNA Seq V2) #9 gbm_tcga_mrna_U133 Samples with mRNA data (U133 microarray) #10 gbm_tcga_cnaseq Samples with mutation and CNA data #11 gbm_tcga_sequenced Samples with mutation data #12 gbm_tcga_rppa Samples with protein data (RPPA) (mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]) # gbm_tcga_all (getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)) #BRCA1 BRCA2 #TCGA.02.0001.01 -1 1 #TCGA.02.0003.01 0 0 #TCGA.02.0006.01 0 -1 (getProfileData(mycgds,c('BRCA1'),c("gbm_tcga_mrna","gbm_tcga_gistic"),mycaselist)) #gbm_tcga_mrna gbm_tcga_gistic #TCGA.02.0001.01 NaN -1 #TCGA.02.0003.01 NaN 0 #TCGA.02.0006.01 NaN 0 (myclinicaldata = getClinicalData(mycgds,mycaselist)[1:3,1:3]) #AGE CANCER_TYPE CANCER_TYPE_DETAILED #TCGA.32.4213.01 47 Glioma Glioblastoma Multiforme #TCGA.14.1452.01 60 Glioma Glioblastoma Multiforme #TCGA.08.0509.01 63 Glioma Glioblastoma Multiforme browseVignettes("cgdsr")