Get or Check TCGA Available ProjectID, DataType and FileType
Usage
availTCGA(which = c("all", "ProjectID", "DataType", "FileType"))Author
Shixiang Wang w_shixiang@163.com
Examples
# \donttest{
availTCGA("all")
#> Note not all projects have listed data types and file types, you can use showTCGA function to check if exist
#> $ProjectID
#> [1] "OV" "KIRC" "LGG" "KIRP" "PANCAN" "CHOL"
#> [7] "COADREAD" "ACC" "CESC" "READ" "SARC" "DLBC"
#> [13] "PRAD" "LUNG" "LIHC" "KICH" "HNSC" "PCPG"
#> [19] "ESCA" "THCA" "LUAD" "LAML" "BLCA" "SKCM"
#> [25] "LUSC" "TGCT" "PAAD" "GBM" "STAD" "MESO"
#> [31] "UVM" "GBMLGG" "THYM" "UCEC" "BRCA" "UCS"
#> [37] "COAD" "FPPP"
#>
#> $DataType
#> [1] "DNA Methylation"
#> [2] "Gene Level Copy Number"
#> [3] "Phenotype"
#> [4] "Protein Expression RPPA"
#> [5] "Gene Expression Array"
#> [6] "Gene Expression RNASeq"
#> [7] "Copy Number Segments"
#> [8] "miRNA Mature Strand Expression RNASeq"
#> [9] "Exon Expression RNASeq"
#> [10] "Transcription Factor Regulatory Impact"
#> [11] "PARADIGM Pathway Activity"
#> [12] NA
#> [13] "Gene Somatic Non-silent Mutation"
#> [14] "Somatic Mutation"
#> [15] "Signatures"
#> [16] "iCluster"
#>
#> $FileType
#> [1] "Methylation27K"
#> [2] "Methylation450K"
#> [3] "Gistic2"
#> [4] "Clinical Information"
#> [5] "RPPA normalized by RBN"
#> [6] "Affymetrix U133A Microarray"
#> [7] "IlluminaHiSeq RNASeqV2 in percentile rank"
#> [8] "IlluminaHiSeq RNASeqV2 pancan normalized"
#> [9] "IlluminaHiSeq RNASeqV2"
#> [10] "IlluminaHiSeq RNASeq"
#> [11] "After remove germline cnv"
#> [12] "Agilent 244K Microarray"
#> [13] "Gistic2 thresholded"
#> [14] "RPPA"
#> [15] "Before remove germline cnv"
#> [16] "Gene Expression Subtype"
#> [17] "RABIT Use Agilent 244K Microarray"
#> [18] "RABIT Use Affymetrix U133A Microarray"
#> [19] "Platform-corrected PANCAN12 dataset"
#> [20] NA
#> [21] "IlluminaGA RNASeq"
#> [22] "RABIT Use IlluminaHiSeq RNASeqV2"
#> [23] "RABIT Use IlluminaHiSeq RNASeq"
#> [24] "MethylMix"
#> [25] "IlluminaGA RNASeqV2"
#> [26] "broad automated"
#> [27] "wustl automated"
#> [28] "RABIT Use IlluminaGA RNASeqV2"
#> [29] "RABIT Use IlluminaGA RNASeq"
#> [30] "Batch effects normalized"
#> [31] "MC3 Public Version"
#> [32] "TCGA Sample Type and Primary Disease"
#> [33] "RPPA pancan normalized"
#> [34] "Tumor copy number"
#> [35] "Genome-wide DNA Damage Footprint HRD Score"
#> [36] "TCGA Molecular Subtype"
#> [37] "iCluster cluster assignments"
#> [38] "iCluster latent variables"
#> [39] "RNA based StemnessScore"
#> [40] "DNA methylation based StemnessScore"
#> [41] "Pancan Gene Programs"
#> [42] "Immune Model Based Subtype"
#> [43] "Immune Signature Scores"
#>
# }