#查看有多少不同的癌症数据集
library(cgdsr)
library(DT)
mycgds <- CGDS("http://www.cbioportal.org/public-portal/")
all_TCGA_studies <- getCancerStudies(mycgds)
DT::datatable(all_TCGA_studies)
#查看任意数据集的样本列表方式
stad2014<-"stad_tcga_pub"
all_tables<-getCaseLists(mycgds,stad2014)
DT::datatable(all_tables[,1:3])
#查看任意数据集的数据形式
all_dataset<-getGeneticProfiles(mycgds,stad2014)
DT::datatable(all_dataset,extensions = 'FixedColumns',options = list(scrollX = TRUE,fixedColumns = TRUE))
#获取一个基因的一个profile
my_dataset<-"stad_tcga_pub_rna_seq_v2_mrna"##数据类型
my_table<-"stad_tcga_pub_all"##选取一样本
BRCA1 <- getProfileData(mycgds,"BRCA1", my_dataset, my_table)##在mycgds链接里，获得my_table样本的BRCA1基因的my_dataset数据类型
data <- getProfileData(mycgds,c("BRCA1","BRCA2"), my_dataset, my_table)##获取多个基因的相同profile
#选定样本获取临床信息
clinicaldata<-getClinicalData(mycgds,my_table)#此链接下该样本的临床信息
#下载点突变信息
library(cgdsr)library(DT)
mycgds <- CGDS("http://www.cbioportal.org/public-portal/")
mutGene=c("TP53","UGT2B7","CYP3A4")
mut_df<-getProfileData(mycgds,mutGene,"gbm_tcga_mutations","gbm_tcga_sequenced")
mut_df<-apply(mut_df,2,as.factor)
mut_df[mut_df=="NaN"]=""
mut_df[is.na(mut_df)]=""
mut_df[mut_df != ""]="MUT"
#拷贝数变异数据
cna<-getProfileData(mycgds,mutGene,"gbm_tcga_gistic","gbm_tcga_sequenced")
cna<-apply(cna,2,function(x) as.character(factor(x,levels = c(-2:2),labels = c("HOMDEL","HETLOSS","DIPLOID","GAIN","AMP"))))
cna[is.na(cna)]=""
cna[cna=="DIPLOID"]=""
DT::datatable(cna)
