TCGAbiolinks - checking bug 367

1 Code

download_htseq_solidNormaldata <- function(selectedcancer){
    print(selectedcancer)
    
    suppressMessages({
        query <- GDCquery(
            project = selectedcancer,
            data.category = "Transcriptome Profiling",
            data.type = "Gene Expression Quantification",
            sample.type = "Solid Tissue Normal",
            workflow.type = "HTSeq - FPKM-UQ")
    })
    if (is.null(query)){
        print(paste0("No FPKM-UQ data of solid normal tissue for ", selectedcancer))
    } else{
        sink(file = "/dev/null") # to remove progress bar from rmd
        GDCdownload(query)
        data <- GDCprepare(query,
                           save = TRUE,
                           save.filename = paste0(selectedcancer,".rda"))
        sink()
        print(data)
        clin <- colData(data)
        df_all <- assay(data)
    }
}

tcga_projects <- TCGAbiolinks:::getGDCprojects()$project_id
mycancertypes <- tcga_projects[grepl("^TCGA-",tcga_projects)] # total 33

download_all <- sapply(mycancertypes[order(mycancertypes)],function(x) download_htseq_solidNormaldata(selectedcancer=x))

## [1] "TCGA-ACC"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-ACC"
## [1] "TCGA-BLCA"

## Downloading data for project TCGA-BLCA

## GDCdownload will download 19 files. A total of 9.617101 MB

## Downloading as: Mon_Nov_25_09_50_22_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## blca subtype information from:doi:10.1016/j.cell.2017.09.007

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-BLCA.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 19 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(19): TCGA-CU-A0YN-11A-11R-A10U-07 TCGA-BT-A20U-11A-11R-A14Y-07
##   ... TCGA-K4-A3WV-11A-21R-A22U-07 TCGA-GC-A3WC-11A-11R-A22U-07
## colData names(238): barcode patient ... subtype_Fusion in TNFRSF21
##   subtype_Fusion in ASIP
## [1] "TCGA-BRCA"

## Downloading data for project TCGA-BRCA

## GDCdownload will download 113 files. A total of 59.697166 MB

## Downloading as: Mon_Nov_25_09_50_45_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## brca subtype information from:doi.org/10.1016/j.ccell.2018.03.014

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-BRCA.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 113 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(113): TCGA-E2-A1LH-11A-22R-A14D-07
##   TCGA-BH-A0DG-11A-43R-A12P-07 ... TCGA-E9-A1RH-11A-34R-A169-07
##   TCGA-BH-A0BW-11A-12R-A115-07
## colData names(83): barcode patient ... subtype_PARADIGM Clusters
##   subtype_Pan-Gyn Clusters
## [1] "TCGA-CESC"

## Downloading data for project TCGA-CESC

## GDCdownload will download 3 files. A total of 1.521645 MB

## Downloading as: Mon_Nov_25_09_51_35_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## cesc subtype information from:doi:10.1038/nature21386

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-CESC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 3 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(3): TCGA-HM-A3JJ-11A-12R-A21T-07 TCGA-FU-A3EO-11A-13R-A213-07
##   TCGA-MY-A5BF-11A-11R-A26T-07
## colData names(127): barcode patient ... subtype_GEXP:APOBEC3H:164668
##   subtype_patient
## [1] "TCGA-CHOL"

## Downloading data for project TCGA-CHOL

## GDCdownload will download 9 files. A total of 4.328599 MB

## Downloading as: Mon_Nov_25_09_51_42_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## chol subtype information from:doi:10.1016/j.celrep.2017.02.033

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-CHOL.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 9 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(9): TCGA-W5-AA2U-11A-11R-A41I-07 TCGA-ZU-A8S4-11A-11R-A41I-07
##   ... TCGA-W5-AA31-11A-11R-A41I-07 TCGA-W5-AA2X-11A-11R-A41I-07
## colData names(204): barcode patient ... subtype_20 subtype_21
## [1] "TCGA-COAD"

## Downloading data for project TCGA-COAD

## Of the 41 files for download 41 already exist.

## All samples have been already downloaded

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## coad subtype information from:doi:10.1038/nature11252

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-COAD.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 41 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(41): TCGA-A6-5665-11A-01R-1653-07 TCGA-AA-3511-11A-01R-1839-07
##   ... TCGA-AZ-6605-11A-01R-1839-07 TCGA-AZ-6601-11A-01R-1774-07
## colData names(107): barcode patient ...
##   subtype_vascular_invasion_present subtype_vital_status
## [1] "TCGA-DLBC"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-DLBC"
## [1] "TCGA-ESCA"

## Downloading data for project TCGA-ESCA

## GDCdownload will download 11 files. A total of 6.146252 MB

## Downloading as: Mon_Nov_25_09_52_05_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## esca subtype information from:doi:10.1038/nature20805

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-ESCA.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 11 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(11): TCGA-IC-A6RE-11A-12R-A336-31 TCGA-V5-AASX-11A-11R-A38D-31
##   ... TCGA-L5-A4OJ-11A-12R-A260-31 TCGA-V5-A7RE-11A-11R-A354-31
## colData names(140): barcode patient ... subtype_GEA-CIN Integrated
##   Cluster - MKL-KNN-4 subtype_GEA-CIN Integrated Cluster - MKL-KNN-7
## [1] "TCGA-GBM"

## Downloading data for project TCGA-GBM

## GDCdownload will download 5 files. A total of 2.658072 MB

## Downloading as: Mon_Nov_25_09_52_15_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## gbm subtype information from:doi:10.1016/j.cell.2015.12.028

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-GBM.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 5 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(5): TCGA-06-0680-11A-32R-A36H-07 TCGA-06-0678-11A-32R-A36H-07
##   TCGA-06-0675-11A-32R-A36H-07 TCGA-06-AABW-11A-31R-A36H-07
##   TCGA-06-0681-11A-41R-A36H-07
## colData names(74): barcode patient ...
##   subtype_Telomere.length.estimate.in.blood.normal..Kb.
##   subtype_Telomere.length.estimate.in.tumor..Kb.
## [1] "TCGA-HNSC"

## Downloading data for project TCGA-HNSC

## GDCdownload will download 44 files. A total of 22.121259 MB

## Downloading as: Mon_Nov_25_09_52_24_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## hnsc subtype information from:doi:10.1038/nature14129

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-HNSC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 44 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(44): TCGA-CV-7097-11A-01R-2016-07 TCGA-CV-7416-11A-01R-2081-07
##   ... TCGA-CV-6955-11A-01R-2016-07 TCGA-CV-6939-11A-01R-1915-07
## colData names(76): barcode patient ... subtype_Copy.Number
##   subtype_PARADIGM
## [1] "TCGA-KICH"

## Downloading data for project TCGA-KICH

## GDCdownload will download 24 files. A total of 12.707799 MB

## Downloading as: Mon_Nov_25_09_52_45_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## kich subtype information from:doi:10.1016/j.ccr.2014.07.014

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-KICH.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 24 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(24): TCGA-KN-8426-11A-01R-2315-07 TCGA-KO-8403-11A-01R-2315-07
##   ... TCGA-KN-8430-11A-01R-2315-07 TCGA-KL-8336-11A-01R-2315-07
## colData names(95): barcode patient ... subtype_Copy.Pattern
##   subtype_Notable.Molecular.Observations
## [1] "TCGA-KIRC"

## Downloading data for project TCGA-KIRC

## GDCdownload will download 72 files. A total of 37.644714 MB

## Downloading as: Mon_Nov_25_09_53_01_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## kirc subtype information from:doi:10.1038/nature12222

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-KIRC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 72 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(72): TCGA-CZ-5458-11A-01R-1503-07 TCGA-CZ-5989-11A-01R-1672-07
##   ... TCGA-CW-6087-11A-01R-1672-07 TCGA-B2-5641-11A-01R-1541-07
## colData names(62): barcode patient ... subtype_mRNA_cluster
##   subtype_microRNA_cluster
## [1] "TCGA-KIRP"

## Downloading data for project TCGA-KIRP

## GDCdownload will download 32 files. A total of 16.829865 MB

## Downloading as: Mon_Nov_25_09_53_31_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## kirp subtype information from:doi:10.1056/NEJMoa1505917

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-KIRP.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 32 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(32): TCGA-P4-A5E8-11A-12R-A28H-07 TCGA-BQ-5894-11A-01R-1592-07
##   ... TCGA-BQ-5884-11A-01R-1592-07 TCGA-GL-6846-11A-01R-1965-07
## colData names(210): barcode patient ... subtype_VHL.copy..log2.normal.
##   subtype_NF2.copy..log2.normal.
## [1] "TCGA-LAML"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-LAML"
## [1] "TCGA-LGG"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-LGG"
## [1] "TCGA-LIHC"

## Downloading data for project TCGA-LIHC

## GDCdownload will download 50 files. A total of 23.991988 MB

## Downloading as: Mon_Nov_25_09_53_52_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-LIHC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 50 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(50): TCGA-EP-A3RK-11A-11R-A22L-07 TCGA-BC-A10T-11A-11R-A131-07
##   ... TCGA-G3-A3CH-11A-11R-A22L-07 TCGA-FV-A3I0-11A-11R-A22L-07
## colData names(63): barcode patient ... name sample.aux
## [1] "TCGA-LUAD"

## Downloading data for project TCGA-LUAD

## GDCdownload will download 59 files. A total of 30.327633 MB

## Downloading as: Mon_Nov_25_09_54_32_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## luad subtype information from:doi:10.1038/nature13385

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-LUAD.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 59 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(59): TCGA-55-6971-11A-01R-1949-07 TCGA-44-6778-11A-01R-1858-07
##   ... TCGA-91-6849-11A-01R-1949-07 TCGA-49-6761-11A-01R-1949-07
## colData names(83): barcode patient ... subtype_Ploidy.ABSOLUTE.calls
##   subtype_Purity.ABSOLUTE.calls
## [1] "TCGA-LUSC"

## Downloading data for project TCGA-LUSC

## GDCdownload will download 49 files. A total of 25.951806 MB

## Downloading as: Mon_Nov_25_09_55_04_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## lusc subtype information from:doi:10.1038/nature11404

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-LUSC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 49 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(49): TCGA-33-6737-11A-01R-1820-07 TCGA-77-7335-11A-01R-2045-07
##   ... TCGA-77-7138-11A-01R-2045-07 TCGA-22-4593-11A-01R-1820-07
## colData names(76): barcode patient ... subtype_Homozygous.Deletions
##   subtype_Expression.Subtype
## [1] "TCGA-MESO"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-MESO"
## [1] "TCGA-OV"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-OV"
## [1] "TCGA-PAAD"

## Downloading data for project TCGA-PAAD

## GDCdownload will download 4 files. A total of 2.134398 MB

## Downloading as: Mon_Nov_25_09_55_35_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## paad subtype information from:doi:10.1016/j.ccell.2017.07.007

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-PAAD.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 4 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(4): TCGA-H6-A45N-11A-12R-A26U-07 TCGA-HV-A5A3-11A-11R-A26U-07
##   TCGA-YB-A89D-11A-11R-A36G-07 TCGA-H6-8124-11A-01R-2404-07
## colData names(119): barcode patient ... subtype_Year of tobacco smoking
##   onset subtype_patient
## [1] "TCGA-PCPG"

## Downloading data for project TCGA-PCPG

## GDCdownload will download 3 files. A total of 1.511128 MB

## Downloading as: Mon_Nov_25_09_56_02_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## pcpg subtype information from:doi:10.1016/j.ccell.2017.01.001

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-PCPG.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 3 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(3): TCGA-SQ-A6I4-11A-11R-A35L-07 TCGA-P8-A5KC-11A-11R-A35K-07
##   TCGA-P8-A5KD-11A-11R-A35K-07
## colData names(150): barcode patient ... subtype_RPPA Cluster
##   subtype_Presence of Adrenal Cortical Cells/Tissue on Pathology
##   Re-review
## [1] "TCGA-PRAD"

## Downloading data for project TCGA-PRAD

## GDCdownload will download 52 files. A total of 27.097879 MB

## Downloading as: Mon_Nov_25_09_56_17_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## prad subtype information from:doi:10.1016/j.cell.2015.10.025

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-PRAD.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 52 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(52): TCGA-EJ-7783-11A-01R-2118-07 TCGA-CH-5761-11A-01R-1580-07
##   ... TCGA-G9-6362-11A-01R-1789-07 TCGA-HC-7740-11A-01R-2118-07
## colData names(145): barcode patient ... subtype_AR_V7_ratio
##   subtype_AR_V7_presence
## [1] "TCGA-READ"

## Downloading data for project TCGA-READ

## GDCdownload will download 10 files. A total of 5.128913 MB

## Downloading as: Mon_Nov_25_09_56_51_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## read subtype information from:doi:10.1038/nature11252

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-READ.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 10 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(10): TCGA-AF-2689-11A-01R-A32Z-07 TCGA-AG-3725-11A-01R-1736-07
##   ... TCGA-AG-3742-11A-01R-1660-07 TCGA-AF-2692-11A-01R-A32Z-07
## colData names(106): barcode patient ...
##   subtype_vascular_invasion_present subtype_vital_status
## [1] "TCGA-SARC"

## Downloading data for project TCGA-SARC

## GDCdownload will download 2 files. A total of 989.131 KB

## Downloading as: Mon_Nov_25_09_57_09_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## sarc subtype information from:doi:10.1016/j.cell.2017.10.014

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-SARC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 2 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(2): TCGA-K1-A3PO-11A-12R-A21T-07 TCGA-FX-A2QS-11A-11R-A21T-07
## colData names(107): barcode patient ... subtype_CIN subtype_Mutation
##   Load
## [1] "TCGA-SKCM"

## Downloading data for project TCGA-SKCM

## GDCdownload will download: 517.985 KB

## Downloading as: 7b98f1f0-ec44-4414-8e1c-0d29a386e45c.FPKM-UQ.txt.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## skcm subtype information from:doi:10.1016/j.cell.2015.05.044

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Accessing www.ensembl.org (mirror useast)

## Downloading genome information (try:1) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-SKCM.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 1 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(1): TCGA-GN-A4U8-11A-11R-A32P-07
## colData names(166): barcode patient ... subtype_DIPYRIM.C.T.n.C.T..mut
##   subtype_SHATTERSEEK_Chromothripsis_calls
## [1] "TCGA-STAD"

## Downloading data for project TCGA-STAD

## GDCdownload will download 32 files. A total of 17.059642 MB

## Downloading as: Mon_Nov_25_09_59_23_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## stad subtype information from:doi:10.1038/nature13480

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-STAD.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 32 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(32): TCGA-BR-6453-11A-01R-1802-13 TCGA-BR-6454-11A-01R-1802-13
##   ... TCGA-CG-5734-11A-01R-1602-13 TCGA-BR-7715-11A-01R-2055-13
## colData names(109): barcode patient ... subtype_CIMP.Category
##   subtype_stringAsFactor
## [1] "TCGA-TGCT"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-TGCT"
## [1] "TCGA-THCA"

## Downloading data for project TCGA-THCA

## GDCdownload will download 58 files. A total of 30.745843 MB

## Downloading as: Mon_Nov_25_09_59_48_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## thca subtype information from:doi:10.1016/j.cell.2014.09.050

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-THCA.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 58 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(58): TCGA-KS-A41J-11A-12R-A23N-07 TCGA-BJ-A2N8-11A-11R-A18C-07
##   ... TCGA-EL-A3ZK-11A-11R-A23N-07 TCGA-BJ-A3PR-11A-11R-A220-07
## colData names(238): barcode patient ... subtype_TERT_AC subtype_TERT_Q
## [1] "TCGA-THYM"

## Downloading data for project TCGA-THYM

## GDCdownload will download 2 files. A total of 1.085485 MB

## Downloading as: Mon_Nov_25_10_00_16_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-THYM.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 2 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(2): TCGA-X7-A8D7-11A-11R-A42C-07 TCGA-X7-A8D6-11A-22R-A42C-07
## colData names(54): barcode patient ... name sample.aux
## [1] "TCGA-UCEC"

## Downloading data for project TCGA-UCEC

## GDCdownload will download 35 files. A total of 18.035498 MB

## Downloading as: Mon_Nov_25_10_00_42_2019.tar.gz

## Starting to add information to samples

##  => Add clinical information to samples

##  => Adding subtype information to samples

## ucec subtype information from:doi:10.1038/nature12113

## Accessing www.ensembl.org to get gene information

## Downloading genome information (try:0) Using: Human genes (GRCh38.p13)

## Cache found

## From the 60483 genes we couldn't map 3971

## Saving file:TCGA-UCEC.rda

## File saved

## class: RangedSummarizedExperiment 
## dim: 56512 35 
## metadata(1): data_release
## assays(1): HTSeq - FPKM-UQ
## rownames(56512): ENSG00000000003 ENSG00000000005 ... ENSG00000281912
##   ENSG00000281920
## rowData names(3): ensembl_gene_id external_gene_name
##   original_ensembl_gene_id
## colnames(35): TCGA-DI-A2QY-11A-11R-A19W-07 TCGA-FL-A1YF-11A-12R-A16F-07
##   ... TCGA-FL-A1YI-11A-11R-A16F-07 TCGA-DI-A2QU-11A-11R-A18M-07
## colData names(78): barcode patient ... subtype_cna_cluster_k4
##   subtype_mrna_expression_cluster
## [1] "TCGA-UCS"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-UCS"
## [1] "TCGA-UVM"
## [1] "No FPKM-UQ data of solid normal tissue for TCGA-UVM"

2 Session information

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.1 (2019-07-05)
##  os       Ubuntu 19.10                
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language en_US                       
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2019-11-25                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  ! package              * version   date       lib
##    annotate               1.64.0    2019-10-29 [1]
##    AnnotationDbi          1.48.0    2019-10-29 [1]
##    aroma.light            3.16.0    2019-10-29 [1]
##    askpass                1.1       2019-01-13 [2]
##    assertthat             0.2.1     2019-03-21 [2]
##    backports              1.1.5     2019-10-02 [2]
##    base64enc              0.1-3     2015-07-28 [2]
##    Biobase              * 2.46.0    2019-10-29 [1]
##    BiocFileCache          1.10.0    2019-10-29 [1]
##    BiocGenerics         * 0.32.0    2019-10-29 [1]
##    BiocParallel         * 1.20.0    2019-10-30 [1]
##    biomaRt                2.42.0    2019-10-29 [1]
##    Biostrings             2.54.0    2019-10-29 [1]
##    bit                    1.1-14    2018-05-29 [2]
##    bit64                  0.9-7     2017-05-08 [2]
##    bitops                 1.0-6     2013-08-17 [2]
##    blob                   1.2.0     2019-07-09 [2]
##    broom                  0.5.2     2019-04-07 [2]
##    callr                  3.3.2     2019-09-22 [2]
##    circlize               0.4.8     2019-09-08 [2]
##    cli                    1.1.0     2019-03-19 [2]
##    clue                   0.3-57    2019-02-25 [2]
##    cluster                2.1.0     2019-06-19 [4]
##    codetools              0.2-16    2018-12-24 [4]
##    colorspace             1.4-1     2019-03-18 [2]
##    ComplexHeatmap         2.3.1     2019-11-09 [2]
##    ConsensusClusterPlus   1.50.0    2019-10-29 [1]
##    crayon                 1.3.4     2017-09-16 [2]
##    curl                   4.2       2019-09-24 [2]
##    data.table             1.12.6    2019-10-18 [1]
##    DBI                    1.0.0     2018-05-02 [2]
##    dbplyr                 1.4.2     2019-06-17 [2]
##    DelayedArray         * 0.12.0    2019-10-29 [1]
##    desc                   1.2.0     2018-05-01 [2]
##    DESeq                  1.38.0    2019-10-29 [1]
##    devtools               2.2.1     2019-09-24 [2]
##    digest                 0.6.22    2019-10-21 [1]
##    doParallel             1.0.15    2019-08-02 [2]
##    downloader             0.4       2015-07-09 [2]
##    dplyr                  0.8.3     2019-07-04 [2]
##    EDASeq                 2.20.0    2019-10-29 [1]
##    edgeR                  3.28.0    2019-10-29 [1]
##    ellipsis               0.3.0     2019-09-20 [2]
##    evaluate               0.14      2019-05-28 [2]
##    foreach                1.4.7     2019-07-27 [2]
##    fs                     1.3.1     2019-05-06 [2]
##    genefilter             1.68.0    2019-10-29 [1]
##    geneplotter            1.64.0    2019-10-29 [1]
##    generics               0.0.2     2018-11-29 [2]
##    GenomeInfoDb         * 1.22.0    2019-10-29 [1]
##    GenomeInfoDbData       1.2.2     2019-11-06 [1]
##    GenomicAlignments      1.22.0    2019-10-29 [1]
##    GenomicFeatures        1.38.0    2019-10-29 [1]
##    GenomicRanges        * 1.38.0    2019-10-29 [1]
##    GetoptLong             0.1.7     2018-06-10 [2]
##    ggplot2                3.2.1     2019-08-10 [2]
##    ggpubr                 0.2.4     2019-11-14 [2]
##    ggrepel                0.8.1     2019-05-07 [2]
##    ggsignif               0.6.0     2019-08-08 [2]
##    ggthemes               4.2.0     2019-05-13 [2]
##    GlobalOptions          0.1.1     2019-09-30 [2]
##    glue                   1.3.1     2019-03-12 [2]
##    gridExtra              2.3       2017-09-09 [2]
##    gtable                 0.3.0     2019-03-25 [1]
##    hms                    0.5.2     2019-10-30 [2]
##    htmltools              0.4.0     2019-10-04 [2]
##    httr                   1.4.1     2019-08-05 [2]
##    hwriter                1.3.2     2014-09-10 [2]
##    IRanges              * 2.20.0    2019-10-29 [1]
##    iterators              1.0.12    2019-07-26 [2]
##    jsonlite               1.6       2018-12-07 [2]
##    km.ci                  0.5-2     2009-08-30 [2]
##    KMsurv                 0.1-5     2012-12-03 [2]
##    knitr                  1.26      2019-11-12 [2]
##    lattice                0.20-38   2018-11-04 [4]
##    latticeExtra           0.6-28    2016-02-09 [2]
##    lazyeval               0.2.2     2019-03-15 [2]
##    lifecycle              0.1.0     2019-08-01 [2]
##    limma                  3.42.0    2019-10-29 [1]
##    locfit                 1.5-9.1   2013-04-20 [2]
##    magrittr               1.5       2014-11-22 [2]
##    matlab                 1.0.2     2014-06-24 [2]
##    Matrix                 1.2-17    2019-03-22 [4]
##    matrixStats          * 0.55.0    2019-09-07 [2]
##    memoise                1.1.0     2017-04-21 [2]
##    mgcv                   1.8-31    2019-11-09 [4]
##    munsell                0.5.0     2018-06-12 [2]
##    nlme                   3.1-142   2019-11-07 [4]
##    openssl                1.4.1     2019-07-18 [2]
##    pillar                 1.4.2     2019-06-29 [2]
##    pkgbuild               1.0.6     2019-10-09 [2]
##    pkgconfig              2.0.3     2019-09-22 [2]
##    pkgload                1.0.2     2018-10-29 [2]
##    plyr                   1.8.4     2016-06-08 [2]
##    png                    0.1-7     2013-12-03 [2]
##    prettyunits            1.0.2     2015-07-13 [2]
##    processx               3.4.1     2019-07-18 [2]
##    progress               1.2.2     2019-05-16 [2]
##    ps                     1.3.0     2018-12-21 [2]
##    purrr                  0.3.3     2019-10-18 [1]
##    R.methodsS3            1.7.1     2016-02-16 [2]
##    R.oo                   1.23.0    2019-11-03 [1]
##    R.utils                2.9.0     2019-06-13 [2]
##    R6                     2.4.1     2019-11-12 [2]
##    rappdirs               0.3.1     2016-03-28 [2]
##    RColorBrewer           1.1-2     2014-12-07 [1]
##    Rcpp                   1.0.3     2019-11-08 [2]
##    RCurl                  1.95-4.12 2019-03-04 [2]
##    readr                  1.3.1     2018-12-21 [2]
##    remotes                2.1.0     2019-06-24 [2]
##    rjson                  0.2.20    2018-06-08 [2]
##    rlang                  0.4.2     2019-11-23 [2]
##    rmarkdown              1.16      2019-10-01 [1]
##    rprojroot              1.3-2     2018-01-03 [2]
##    Rsamtools              2.2.0     2019-10-29 [1]
##    RSQLite                2.1.2     2019-07-24 [2]
##    rstudioapi             0.10      2019-03-19 [2]
##    rtracklayer            1.46.0    2019-10-29 [1]
##    rvest                  0.3.5     2019-11-08 [2]
##    S4Vectors            * 0.24.0    2019-10-29 [1]
##    scales                 1.1.0     2019-11-18 [2]
##    selectr                0.4-2     2019-11-20 [2]
##    sessioninfo            1.1.1     2018-11-05 [2]
##    shape                  1.4.4     2018-02-07 [2]
##    ShortRead              1.44.0    2019-10-29 [1]
##    stringi                1.4.3     2019-03-12 [2]
##    stringr                1.4.0     2019-02-10 [2]
##    SummarizedExperiment * 1.16.0    2019-10-29 [1]
##    survival               3.1-7     2019-11-09 [4]
##    survminer              0.4.6     2019-09-03 [2]
##    survMisc               0.5.5     2018-07-05 [2]
##    sva                    3.34.0    2019-10-29 [1]
##  P TCGAbiolinks         * 2.15.1    2019-11-11 [?]
##    testthat             * 2.3.0     2019-11-05 [2]
##    tibble                 2.1.3     2019-06-06 [2]
##    tidyr                  1.0.0     2019-09-11 [2]
##    tidyselect             0.2.5     2018-10-11 [2]
##    usethis                1.5.1     2019-07-04 [2]
##    vctrs                  0.2.0     2019-07-05 [2]
##    withr                  2.1.2     2018-03-15 [2]
##    xfun                   0.10      2019-10-01 [1]
##    XML                    3.98-1.20 2019-06-06 [2]
##    xml2                   1.2.2     2019-08-09 [2]
##    xtable                 1.8-4     2019-04-21 [2]
##    XVector                0.26.0    2019-10-29 [1]
##    yaml                   2.2.0     2018-07-25 [2]
##    zeallot                0.1.0     2018-01-28 [2]
##    zlibbioc               1.32.0    2019-10-29 [1]
##    zoo                    1.8-6     2019-05-28 [2]
##  source                                  
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##  Bioconductor                            
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  Bioconductor                            
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  Bioconductor                            
##  Bioconductor                            
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  Bioconductor                            
##  CRAN (R 3.6.1)                          
##  CRAN (R 3.6.1)                          
##  Bioconductor                            
##  CRAN (R 3.6.1)                          
## 
## [1] /home/tiagochst/R/x86_64-pc-linux-gnu-library/3.6
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
## 
##  P ── Loaded and on-disk path mismatch.