基本使用
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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")
参考