TCGA-SARC - HTSeq - Counts

library(TCGAbiolinks)

1 Search file

query <- GDCquery(project = "TCGA-SARC",
                  sample.type = "Primary Tumor",
                data.category = "Transcriptome Profiling",
                data.type = "Gene Expression Quantification",
                workflow.type = "HTSeq - Counts")
GDCdownload(query, files.per.chunk = 50)
data <- GDCprepare(query)

2 Data

data

## class: RangedSummarizedExperiment 
## dim: 56512 259 
## metadata(1): data_release
## assays(1): HTSeq - Counts
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(259): TCGA-SI-A71O-01A-12R-A33J-07
##   TCGA-UE-A6QU-01A-12R-A32Q-07 ... TCGA-QQ-A8VH-01A-11R-A37L-07
##   TCGA-SI-A71P-01A-12R-A33J-07
## colData names(110): barcode patient ... paper_CIN paper_Mutation Load