1 Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("curatedTCGAData")

Load packages:

library(curatedTCGAData)
library(MultiAssayExperiment)
library(TCGAutils)

2 Downloading datasets

Checking available cancer codes and assays in TCGA data:

curatedTCGAData(diseaseCode = "*", assays = "*", dry.run = TRUE)
## snapshotDate(): 2020-09-14
## See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
##      ah_id                                      title file_size
## 1    EH558                        ACC_CNASNP-20160128    0.8 Mb
## 2    EH559                        ACC_CNVSNP-20160128    0.2 Mb
## 3    EH561              ACC_GISTIC_AllByGene-20160128    0.3 Mb
## 4   EH2115                  ACC_GISTIC_Peaks-20160128      0 Mb
## 5    EH562      ACC_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 6   EH2116            ACC_Methylation-20160128_assays  236.4 Mb
## 7   EH2117                ACC_Methylation-20160128_se    6.1 Mb
## 8    EH565                  ACC_miRNASeqGene-20160128    0.1 Mb
## 9    EH566                      ACC_Mutation-20160128    0.7 Mb
## 10   EH567               ACC_RNASeq2GeneNorm-20160128      4 Mb
## 11   EH568                     ACC_RPPAArray-20160128    0.1 Mb
## 12   EH570                       BLCA_CNASeq-20160128    0.3 Mb
## 13   EH571                       BLCA_CNASNP-20160128    4.3 Mb
## 14   EH572                       BLCA_CNVSNP-20160128    1.1 Mb
## 15   EH574             BLCA_GISTIC_AllByGene-20160128    0.6 Mb
## 16  EH2118                 BLCA_GISTIC_Peaks-20160128      0 Mb
## 17   EH575     BLCA_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 18  EH2119           BLCA_Methylation-20160128_assays 1283.4 Mb
## 19  EH2120               BLCA_Methylation-20160128_se    6.1 Mb
## 20   EH578                 BLCA_miRNASeqGene-20160128    0.4 Mb
## 21   EH579                     BLCA_Mutation-20160128    3.7 Mb
## 22   EH580              BLCA_RNASeq2GeneNorm-20160128   21.9 Mb
## 23   EH581                   BLCA_RNASeqGene-20160128    2.4 Mb
## 24   EH582                    BLCA_RPPAArray-20160128    0.5 Mb
## 25   EH584                       BRCA_CNASeq-20160128      0 Mb
## 26   EH585                       BRCA_CNASNP-20160128    9.8 Mb
## 27   EH586                       BRCA_CNVSNP-20160128    2.8 Mb
## 28   EH588             BRCA_GISTIC_AllByGene-20160128    1.3 Mb
## 29  EH2121                 BRCA_GISTIC_Peaks-20160128      0 Mb
## 30   EH589     BRCA_GISTIC_ThresholdedByGene-20160128    0.4 Mb
## 31  EH2122  BRCA_Methylation_methyl27-20160128_assays   63.2 Mb
## 32  EH2123      BRCA_Methylation_methyl27-20160128_se    0.4 Mb
## 33  EH2124 BRCA_Methylation_methyl450-20160128_assays 2613.2 Mb
## 34  EH2125     BRCA_Methylation_methyl450-20160128_se    6.1 Mb
## 35   EH593                 BRCA_miRNASeqGene-20160128    0.6 Mb
## 36   EH594                    BRCA_mRNAArray-20160128   27.3 Mb
## 37   EH595                     BRCA_Mutation-20160128    4.5 Mb
## 38   EH596              BRCA_RNASeq2GeneNorm-20160128   64.5 Mb
## 39   EH597                   BRCA_RNASeqGene-20160128     30 Mb
## 40   EH598                    BRCA_RPPAArray-20160128    1.6 Mb
## 41   EH600                       CESC_CNASeq-20160128    0.1 Mb
## 42   EH601                       CESC_CNASNP-20160128    2.3 Mb
## 43   EH602                       CESC_CNVSNP-20160128    0.6 Mb
## 44   EH604             CESC_GISTIC_AllByGene-20160128    0.5 Mb
## 45  EH2126                 CESC_GISTIC_Peaks-20160128      0 Mb
## 46   EH605     CESC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 47  EH2127           CESC_Methylation-20160128_assays  921.2 Mb
## 48  EH2128               CESC_Methylation-20160128_se    6.1 Mb
## 49   EH608                 CESC_miRNASeqGene-20160128    0.3 Mb
## 50   EH609                     CESC_Mutation-20160128      2 Mb
## 51   EH610              CESC_RNASeq2GeneNorm-20160128   16.1 Mb
## 52   EH611                    CESC_RPPAArray-20160128    0.3 Mb
## 53   EH613                       CHOL_CNASNP-20160128    0.4 Mb
## 54   EH614                       CHOL_CNVSNP-20160128    0.1 Mb
## 55   EH616             CHOL_GISTIC_AllByGene-20160128    0.3 Mb
## 56  EH2129                 CHOL_GISTIC_Peaks-20160128      0 Mb
## 57   EH617     CHOL_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 58  EH2130           CHOL_Methylation-20160128_assays  132.1 Mb
## 59  EH2131               CHOL_Methylation-20160128_se    6.1 Mb
## 60   EH620                 CHOL_miRNASeqGene-20160128    0.1 Mb
## 61   EH621                     CHOL_Mutation-20160128    0.2 Mb
## 62   EH622              CHOL_RNASeq2GeneNorm-20160128    2.4 Mb
## 63   EH623                    CHOL_RPPAArray-20160128    0.1 Mb
## 64   EH625                       COAD_CNASeq-20160128    0.3 Mb
## 65   EH626                       COAD_CNASNP-20160128    3.9 Mb
## 66   EH627                       COAD_CNVSNP-20160128    0.9 Mb
## 67   EH629             COAD_GISTIC_AllByGene-20160128    0.5 Mb
## 68  EH2132                 COAD_GISTIC_Peaks-20160128      0 Mb
## 69   EH630     COAD_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 70  EH2133  COAD_Methylation_methyl27-20160128_assays   37.2 Mb
## 71  EH2134      COAD_Methylation_methyl27-20160128_se    0.4 Mb
## 72  EH2135 COAD_Methylation_methyl450-20160128_assays  983.8 Mb
## 73  EH2136     COAD_Methylation_methyl450-20160128_se    6.1 Mb
## 74   EH634                 COAD_miRNASeqGene-20160128    0.2 Mb
## 75   EH635                    COAD_mRNAArray-20160128    8.1 Mb
## 76   EH636                     COAD_Mutation-20160128    1.2 Mb
## 77   EH637              COAD_RNASeq2GeneNorm-20160128    8.8 Mb
## 78   EH638                   COAD_RNASeqGene-20160128    0.4 Mb
## 79   EH639                    COAD_RPPAArray-20160128    0.6 Mb
## 80   EH641                       DLBC_CNASNP-20160128    0.4 Mb
## 81   EH642                       DLBC_CNVSNP-20160128    0.1 Mb
## 82   EH644             DLBC_GISTIC_AllByGene-20160128    0.2 Mb
## 83  EH2137                 DLBC_GISTIC_Peaks-20160128      0 Mb
## 84   EH645     DLBC_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 85  EH2138           DLBC_Methylation-20160128_assays  141.8 Mb
## 86  EH2139               DLBC_Methylation-20160128_se    6.1 Mb
## 87   EH648                 DLBC_miRNASeqGene-20160128    0.1 Mb
## 88   EH649                     DLBC_Mutation-20160128    0.7 Mb
## 89   EH650              DLBC_RNASeq2GeneNorm-20160128    2.5 Mb
## 90   EH651                    DLBC_RPPAArray-20160128    0.1 Mb
## 91   EH653                       ESCA_CNASeq-20160128    0.2 Mb
## 92   EH654                       ESCA_CNASNP-20160128    1.8 Mb
## 93   EH655                       ESCA_CNVSNP-20160128    0.7 Mb
## 94   EH657             ESCA_GISTIC_AllByGene-20160128    0.5 Mb
## 95  EH2140                 ESCA_GISTIC_Peaks-20160128      0 Mb
## 96   EH658     ESCA_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 97  EH2141           ESCA_Methylation-20160128_assays  596.9 Mb
## 98  EH2142               ESCA_Methylation-20160128_se    6.1 Mb
## 99   EH661                 ESCA_miRNASeqGene-20160128    0.2 Mb
## 100  EH662                     ESCA_Mutation-20160128    2.8 Mb
## 101  EH663              ESCA_RNASeq2GeneNorm-20160128   10.8 Mb
## 102  EH664                   ESCA_RNASeqGene-20160128      8 Mb
## 103  EH665                    ESCA_RPPAArray-20160128    0.2 Mb
## 104  EH667            GBM_CNACGH_CGH_hg_244a-20160128    0.7 Mb
## 105  EH668     GBM_CNACGH_CGH_hg_415k_g4124a-20160128    0.5 Mb
## 106  EH669                        GBM_CNASNP-20160128    5.2 Mb
## 107  EH670                        GBM_CNVSNP-20160128    1.5 Mb
## 108  EH672              GBM_GISTIC_AllByGene-20160128    0.7 Mb
## 109 EH2143                  GBM_GISTIC_Peaks-20160128      0 Mb
## 110  EH673      GBM_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 111 EH2144   GBM_Methylation_methyl27-20160128_assays   52.4 Mb
## 112 EH2145       GBM_Methylation_methyl27-20160128_se    0.4 Mb
## 113 EH2146  GBM_Methylation_methyl450-20160128_assays  455.1 Mb
## 114 EH2147      GBM_Methylation_methyl450-20160128_se    6.1 Mb
## 115  EH677                    GBM_miRNAArray-20160128    2.1 Mb
## 116  EH678                  GBM_miRNASeqGene-20160128      0 Mb
## 117  EH679                GBM_mRNAArray_huex-20160128   56.3 Mb
## 118 EH2148         GBM_mRNAArray_TX_g4502a_1-20160128   22.5 Mb
## 119  EH680           GBM_mRNAArray_TX_g4502a-20160128    5.7 Mb
## 120  EH681      GBM_mRNAArray_TX_ht_hg_u133a-20160128   44.7 Mb
## 121  EH682                      GBM_Mutation-20160128    2.1 Mb
## 122  EH683               GBM_RNASeq2GeneNorm-20160128    8.6 Mb
## 123  EH684                     GBM_RPPAArray-20160128    0.4 Mb
## 124  EH686                       HNSC_CNASeq-20160128    0.3 Mb
## 125  EH687                       HNSC_CNASNP-20160128    4.2 Mb
## 126  EH688                       HNSC_CNVSNP-20160128    1.1 Mb
## 127  EH690             HNSC_GISTIC_AllByGene-20160128    0.6 Mb
## 128 EH2149                 HNSC_GISTIC_Peaks-20160128      0 Mb
## 129  EH691     HNSC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 130 EH2150           HNSC_Methylation-20160128_assays 1714.7 Mb
## 131 EH2151               HNSC_Methylation-20160128_se    6.1 Mb
## 132  EH694                 HNSC_miRNASeqGene-20160128    0.4 Mb
## 133  EH695                     HNSC_Mutation-20160128    4.8 Mb
## 134  EH696              HNSC_RNASeq2GeneNorm-20160128   29.5 Mb
## 135  EH697                   HNSC_RNASeqGene-20160128   10.3 Mb
## 136  EH698                    HNSC_RPPAArray-20160128    0.3 Mb
## 137  EH700                       KICH_CNASNP-20160128    0.5 Mb
## 138  EH701                       KICH_CNVSNP-20160128    0.1 Mb
## 139  EH703             KICH_GISTIC_AllByGene-20160128    0.2 Mb
## 140 EH2152                 KICH_GISTIC_Peaks-20160128      0 Mb
## 141  EH704     KICH_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 142 EH2153           KICH_Methylation-20160128_assays    195 Mb
## 143 EH2154               KICH_Methylation-20160128_se    6.1 Mb
## 144  EH707                 KICH_miRNASeqGene-20160128    0.1 Mb
## 145  EH708                     KICH_Mutation-20160128    0.1 Mb
## 146  EH709              KICH_RNASeq2GeneNorm-20160128    4.9 Mb
## 147  EH710                    KICH_RPPAArray-20160128    0.1 Mb
## 148  EH712                       KIRC_CNASNP-20160128    4.1 Mb
## 149  EH713                       KIRC_CNVSNP-20160128    0.8 Mb
## 150  EH715             KIRC_GISTIC_AllByGene-20160128    0.5 Mb
## 151 EH2155                 KIRC_GISTIC_Peaks-20160128      0 Mb
## 152  EH716     KIRC_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 153 EH2156  KIRC_Methylation_methyl27-20160128_assays   76.8 Mb
## 154 EH2157      KIRC_Methylation_methyl27-20160128_se    0.4 Mb
## 155 EH2158 KIRC_Methylation_methyl450-20160128_assays 1418.8 Mb
## 156 EH2159     KIRC_Methylation_methyl450-20160128_se    6.1 Mb
## 157  EH720                 KIRC_miRNASeqGene-20160128    0.2 Mb
## 158  EH721                    KIRC_mRNAArray-20160128    3.5 Mb
## 159  EH722                     KIRC_Mutation-20160128    0.4 Mb
## 160  EH723              KIRC_RNASeq2GeneNorm-20160128   32.2 Mb
## 161  EH724                   KIRC_RNASeqGene-20160128   18.2 Mb
## 162  EH725                    KIRC_RPPAArray-20160128    0.8 Mb
## 163  EH727                       KIRP_CNASNP-20160128    2.6 Mb
## 164  EH728                       KIRP_CNVSNP-20160128    0.5 Mb
## 165  EH730             KIRP_GISTIC_AllByGene-20160128    0.3 Mb
## 166 EH2160                 KIRP_GISTIC_Peaks-20160128      0 Mb
## 167  EH731     KIRP_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 168 EH2161  KIRP_Methylation_methyl27-20160128_assays    3.9 Mb
## 169 EH2162      KIRP_Methylation_methyl27-20160128_se    0.4 Mb
## 170 EH2163 KIRP_Methylation_methyl450-20160128_assays    948 Mb
## 171 EH2164     KIRP_Methylation_methyl450-20160128_se    6.1 Mb
## 172  EH735                 KIRP_miRNASeqGene-20160128    0.3 Mb
## 173  EH736                    KIRP_mRNAArray-20160128    0.9 Mb
## 174  EH737                     KIRP_Mutation-20160128    0.5 Mb
## 175  EH738              KIRP_RNASeq2GeneNorm-20160128   16.7 Mb
## 176  EH739                   KIRP_RNASeqGene-20160128    0.6 Mb
## 177  EH740                    KIRP_RPPAArray-20160128    0.3 Mb
## 178  EH742                       LAML_CNASNP-20160128    7.6 Mb
## 179  EH743                       LAML_CNVSNP-20160128    0.3 Mb
## 180 EH2538             LAML_GISTIC_AllByGene-20160128    0.3 Mb
## 181 EH2539                 LAML_GISTIC_Peaks-20160128      0 Mb
## 182 EH2540     LAML_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 183 EH2166  LAML_Methylation_methyl27-20160128_assays   35.6 Mb
## 184 EH2167      LAML_Methylation_methyl27-20160128_se    0.4 Mb
## 185 EH2168 LAML_Methylation_methyl450-20160128_assays  572.8 Mb
## 186 EH2169     LAML_Methylation_methyl450-20160128_se    6.1 Mb
## 187  EH748                     LAML_Mutation-20160128    0.2 Mb
## 188  EH749              LAML_RNASeq2GeneNorm-20160128    8.1 Mb
## 189  EH750                   LAML_RNASeqGene-20160128    5.4 Mb
## 190  EH752                        LGG_CNASeq-20160128    0.1 Mb
## 191  EH753                        LGG_CNASNP-20160128    3.3 Mb
## 192  EH754                        LGG_CNVSNP-20160128    0.8 Mb
## 193  EH756              LGG_GISTIC_AllByGene-20160128    0.5 Mb
## 194 EH2170                  LGG_GISTIC_Peaks-20160128      0 Mb
## 195  EH757      LGG_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 196 EH2171            LGG_Methylation-20160128_assays 1564.1 Mb
## 197 EH2172                LGG_Methylation-20160128_se    6.1 Mb
## 198  EH760                  LGG_miRNASeqGene-20160128    0.4 Mb
## 199  EH761                     LGG_mRNAArray-20160128    1.7 Mb
## 200  EH762                      LGG_Mutation-20160128    0.2 Mb
## 201  EH763               LGG_RNASeq2GeneNorm-20160128   28.3 Mb
## 202  EH764                     LGG_RPPAArray-20160128    0.6 Mb
## 203  EH766                       LIHC_CNASNP-20160128    3.1 Mb
## 204  EH767                       LIHC_CNVSNP-20160128      1 Mb
## 205  EH769             LIHC_GISTIC_AllByGene-20160128    0.6 Mb
## 206 EH2173                 LIHC_GISTIC_Peaks-20160128      0 Mb
## 207  EH770     LIHC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 208 EH2174           LIHC_Methylation-20160128_assays 1267.8 Mb
## 209 EH2175               LIHC_Methylation-20160128_se    6.1 Mb
## 210  EH773                 LIHC_miRNASeqGene-20160128    0.3 Mb
## 211  EH774                     LIHC_Mutation-20160128    0.9 Mb
## 212  EH775              LIHC_RNASeq2GeneNorm-20160128   20.6 Mb
## 213  EH776                   LIHC_RNASeqGene-20160128    0.9 Mb
## 214  EH777                    LIHC_RPPAArray-20160128    0.3 Mb
## 215  EH779                       LUAD_CNASeq-20160128    3.8 Mb
## 216  EH780                       LUAD_CNASNP-20160128    4.2 Mb
## 217  EH781                       LUAD_CNVSNP-20160128    1.2 Mb
## 218  EH783             LUAD_GISTIC_AllByGene-20160128    0.7 Mb
## 219 EH2176                 LUAD_GISTIC_Peaks-20160128      0 Mb
## 220  EH784     LUAD_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 221 EH2177  LUAD_Methylation_methyl27-20160128_assays   16.4 Mb
## 222 EH2178      LUAD_Methylation_methyl27-20160128_se    0.4 Mb
## 223 EH2179 LUAD_Methylation_methyl450-20160128_assays 1452.7 Mb
## 224 EH2180     LUAD_Methylation_methyl450-20160128_se    6.1 Mb
## 225  EH788                 LUAD_miRNASeqGene-20160128    0.4 Mb
## 226  EH789                    LUAD_mRNAArray-20160128    1.6 Mb
## 227  EH790                     LUAD_Mutation-20160128    6.7 Mb
## 228  EH791              LUAD_RNASeq2GeneNorm-20160128   29.8 Mb
## 229  EH792                   LUAD_RNASeqGene-20160128    5.6 Mb
## 230  EH793                    LUAD_RPPAArray-20160128    0.6 Mb
## 231  EH795                       LUSC_CNACGH-20160128    0.7 Mb
## 232  EH796                       LUSC_CNASNP-20160128    4.7 Mb
## 233  EH797                       LUSC_CNVSNP-20160128    1.4 Mb
## 234  EH799             LUSC_GISTIC_AllByGene-20160128    0.7 Mb
## 235 EH2181                 LUSC_GISTIC_Peaks-20160128      0 Mb
## 236  EH800     LUSC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 237 EH2182  LUSC_Methylation_methyl27-20160128_assays   29.5 Mb
## 238 EH2183      LUSC_Methylation_methyl27-20160128_se    0.4 Mb
## 239 EH2184 LUSC_Methylation_methyl450-20160128_assays 1218.4 Mb
## 240 EH2185     LUSC_Methylation_methyl450-20160128_se    6.1 Mb
## 241  EH804                 LUSC_miRNASeqGene-20160128    0.3 Mb
## 242  EH805               LUSC_mRNAArray_huex-20160128   14.8 Mb
## 243  EH806          LUSC_mRNAArray_TX_g4502a-20160128    7.2 Mb
## 244  EH807     LUSC_mRNAArray_TX_ht_hg_u133a-20160128   11.4 Mb
## 245  EH808                     LUSC_Mutation-20160128    5.7 Mb
## 246  EH809              LUSC_RNASeq2GeneNorm-20160128   29.2 Mb
## 247  EH810                   LUSC_RNASeqGene-20160128    8.4 Mb
## 248  EH811                    LUSC_RPPAArray-20160128    0.5 Mb
## 249  EH813                       MESO_CNASNP-20160128    0.8 Mb
## 250  EH814                       MESO_CNVSNP-20160128    0.2 Mb
## 251  EH816             MESO_GISTIC_AllByGene-20160128    0.3 Mb
## 252 EH2186                 MESO_GISTIC_Peaks-20160128      0 Mb
## 253  EH817     MESO_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 254 EH2187           MESO_Methylation-20160128_assays  257.2 Mb
## 255 EH2188               MESO_Methylation-20160128_se    6.1 Mb
## 256  EH820                 MESO_miRNASeqGene-20160128    0.1 Mb
## 257  EH821              MESO_RNASeq2GeneNorm-20160128    4.6 Mb
## 258  EH822                    MESO_RPPAArray-20160128    0.1 Mb
## 259  EH824             OV_CNACGH_CGH_hg_244a-20160128    1.1 Mb
## 260  EH825      OV_CNACGH_CGH_hg_415k_g4124a-20160128    2.2 Mb
## 261  EH826                         OV_CNASNP-20160128    8.2 Mb
## 262  EH827                         OV_CNVSNP-20160128    2.7 Mb
## 263  EH829               OV_GISTIC_AllByGene-20160128    1.2 Mb
## 264 EH2189                   OV_GISTIC_Peaks-20160128      0 Mb
## 265  EH830       OV_GISTIC_ThresholdedByGene-20160128    0.4 Mb
## 266 EH2190    OV_Methylation_methyl27-20160128_assays  108.7 Mb
## 267 EH2191        OV_Methylation_methyl27-20160128_se    0.4 Mb
## 268 EH2192   OV_Methylation_methyl450-20160128_assays   29.6 Mb
## 269 EH2193       OV_Methylation_methyl450-20160128_se    6.1 Mb
## 270  EH834                     OV_miRNAArray-20160128    3.2 Mb
## 271  EH835                   OV_miRNASeqGene-20160128    0.3 Mb
## 272  EH836                 OV_mRNAArray_huex-20160128   75.2 Mb
## 273 EH2194          OV_mRNAArray_TX_g4502a_1-20160128   25.2 Mb
## 274  EH837            OV_mRNAArray_TX_g4502a-20160128    1.9 Mb
## 275  EH838       OV_mRNAArray_TX_ht_hg_u133a-20160128   44.6 Mb
## 276  EH839                       OV_Mutation-20160128    0.5 Mb
## 277  EH840                OV_RNASeq2GeneNorm-20160128   16.7 Mb
## 278  EH841                     OV_RNASeqGene-20160128   10.4 Mb
## 279  EH842                      OV_RPPAArray-20160128    0.7 Mb
## 280  EH844                       PAAD_CNASNP-20160128    1.7 Mb
## 281  EH845                       PAAD_CNVSNP-20160128    0.4 Mb
## 282  EH847             PAAD_GISTIC_AllByGene-20160128    0.4 Mb
## 283 EH2195                 PAAD_GISTIC_Peaks-20160128      0 Mb
## 284  EH848     PAAD_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 285 EH2196           PAAD_Methylation-20160128_assays  575.8 Mb
## 286 EH2197               PAAD_Methylation-20160128_se    6.1 Mb
## 287  EH851                 PAAD_miRNASeqGene-20160128    0.2 Mb
## 288  EH852                     PAAD_Mutation-20160128    6.8 Mb
## 289  EH853              PAAD_RNASeq2GeneNorm-20160128    9.7 Mb
## 290  EH854                    PAAD_RPPAArray-20160128    0.2 Mb
## 291  EH856                       PCPG_CNASNP-20160128    2.6 Mb
## 292  EH857                       PCPG_CNVSNP-20160128    0.3 Mb
## 293  EH859             PCPG_GISTIC_AllByGene-20160128    0.3 Mb
## 294 EH2198                 PCPG_GISTIC_Peaks-20160128      0 Mb
## 295  EH860     PCPG_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 296 EH2199           PCPG_Methylation-20160128_assays  552.9 Mb
## 297 EH2200               PCPG_Methylation-20160128_se    6.1 Mb
## 298  EH863                 PCPG_miRNASeqGene-20160128    0.2 Mb
## 299  EH864                     PCPG_Mutation-20160128    0.6 Mb
## 300  EH865              PCPG_RNASeq2GeneNorm-20160128    9.6 Mb
## 301  EH866                    PCPG_RPPAArray-20160128    0.1 Mb
## 302  EH868                       PRAD_CNASeq-20160128    0.2 Mb
## 303  EH869                       PRAD_CNASNP-20160128    4.9 Mb
## 304  EH870                       PRAD_CNVSNP-20160128    1.2 Mb
## 305  EH872             PRAD_GISTIC_AllByGene-20160128    0.6 Mb
## 306 EH2201                 PRAD_GISTIC_Peaks-20160128      0 Mb
## 307  EH873     PRAD_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 308 EH2202           PRAD_Methylation-20160128_assays 1622.5 Mb
## 309 EH2203               PRAD_Methylation-20160128_se    6.1 Mb
## 310  EH876                 PRAD_miRNASeqGene-20160128    0.4 Mb
## 311  EH877                     PRAD_Mutation-20160128    1.4 Mb
## 312  EH878              PRAD_RNASeq2GeneNorm-20160128   28.9 Mb
## 313  EH879                    PRAD_RPPAArray-20160128    0.5 Mb
## 314  EH881                       READ_CNASeq-20160128    0.4 Mb
## 315  EH882                       READ_CNASNP-20160128    1.4 Mb
## 316  EH883                       READ_CNVSNP-20160128    0.4 Mb
## 317  EH885             READ_GISTIC_AllByGene-20160128    0.3 Mb
## 318 EH2204                 READ_GISTIC_Peaks-20160128      0 Mb
## 319  EH886     READ_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 320 EH2205  READ_Methylation_methyl27-20160128_assays   13.5 Mb
## 321 EH2206      READ_Methylation_methyl27-20160128_se    0.4 Mb
## 322 EH2207 READ_Methylation_methyl450-20160128_assays  313.3 Mb
## 323 EH2208     READ_Methylation_methyl450-20160128_se    6.1 Mb
## 324  EH890                 READ_miRNASeqGene-20160128    0.1 Mb
## 325  EH891                    READ_mRNAArray-20160128    3.5 Mb
## 326  EH892                     READ_Mutation-20160128    0.4 Mb
## 327  EH893              READ_RNASeq2GeneNorm-20160128    3.5 Mb
## 328  EH894                   READ_RNASeqGene-20160128    2.1 Mb
## 329  EH895                    READ_RPPAArray-20160128    0.2 Mb
## 330  EH897                       SARC_CNASNP-20160128    3.1 Mb
## 331  EH898                       SARC_CNVSNP-20160128    1.1 Mb
## 332  EH900             SARC_GISTIC_AllByGene-20160128    0.6 Mb
## 333 EH2209                 SARC_GISTIC_Peaks-20160128      0 Mb
## 334  EH901     SARC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 335 EH2210           SARC_Methylation-20160128_assays  794.3 Mb
## 336 EH2211               SARC_Methylation-20160128_se    6.1 Mb
## 337  EH904                 SARC_miRNASeqGene-20160128    0.2 Mb
## 338  EH905                     SARC_Mutation-20160128    1.1 Mb
## 339  EH906              SARC_RNASeq2GeneNorm-20160128   13.6 Mb
## 340  EH907                    SARC_RPPAArray-20160128    0.3 Mb
## 341 EH1029                       SKCM_CNASeq-20160128    0.3 Mb
## 342 EH1030                       SKCM_CNASNP-20160128    3.8 Mb
## 343 EH1031                       SKCM_CNVSNP-20160128    1.1 Mb
## 344 EH2541             SKCM_GISTIC_AllByGene-20160128    0.5 Mb
## 345 EH2542                 SKCM_GISTIC_Peaks-20160128      0 Mb
## 346 EH2543     SKCM_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 347 EH2213           SKCM_Methylation-20160128_assays 1403.5 Mb
## 348 EH2214               SKCM_Methylation-20160128_se    6.1 Mb
## 349 EH1033                 SKCM_miRNASeqGene-20160128    0.4 Mb
## 350 EH1034                     SKCM_Mutation-20160128   26.7 Mb
## 351 EH1035              SKCM_RNASeq2GeneNorm-20160128   24.5 Mb
## 352 EH1036                    SKCM_RPPAArray-20160128    0.6 Mb
## 353  EH920                       STAD_CNASeq-20160128    0.3 Mb
## 354  EH921                       STAD_CNASNP-20160128    3.8 Mb
## 355  EH922                       STAD_CNVSNP-20160128    1.2 Mb
## 356  EH924             STAD_GISTIC_AllByGene-20160128    0.7 Mb
## 357 EH2215                 STAD_GISTIC_Peaks-20160128      0 Mb
## 358  EH925     STAD_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 359 EH2216  STAD_Methylation_methyl27-20160128_assays   13.5 Mb
## 360 EH2217      STAD_Methylation_methyl27-20160128_se    0.4 Mb
## 361 EH2218 STAD_Methylation_methyl450-20160128_assays 1172.9 Mb
## 362 EH2219     STAD_Methylation_methyl450-20160128_se    6.1 Mb
## 363  EH929                 STAD_miRNASeqGene-20160128    0.3 Mb
## 364  EH930                     STAD_Mutation-20160128   13.2 Mb
## 365  EH931              STAD_RNASeq2GeneNorm-20160128   23.9 Mb
## 366  EH932                   STAD_RNASeqGene-20160128    1.6 Mb
## 367  EH933                    STAD_RPPAArray-20160128    0.5 Mb
## 368  EH935                       TGCT_CNASNP-20160128    1.2 Mb
## 369  EH936                       TGCT_CNVSNP-20160128    0.3 Mb
## 370  EH938             TGCT_GISTIC_AllByGene-20160128    0.3 Mb
## 371 EH2220                 TGCT_GISTIC_Peaks-20160128      0 Mb
## 372  EH939     TGCT_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 373 EH2221           TGCT_Methylation-20160128_assays  411.3 Mb
## 374 EH2222               TGCT_Methylation-20160128_se    6.1 Mb
## 375  EH942                 TGCT_miRNASeqGene-20160128    0.2 Mb
## 376  EH943                     TGCT_Mutation-20160128    0.5 Mb
## 377  EH944              TGCT_RNASeq2GeneNorm-20160128    7.4 Mb
## 378  EH945                    TGCT_RPPAArray-20160128    0.2 Mb
## 379  EH947                       THCA_CNASeq-20160128      0 Mb
## 380  EH948                       THCA_CNASNP-20160128    3.1 Mb
## 381  EH949                       THCA_CNVSNP-20160128    0.5 Mb
## 382  EH951             THCA_GISTIC_AllByGene-20160128    0.3 Mb
## 383 EH2223                 THCA_GISTIC_Peaks-20160128      0 Mb
## 384  EH952     THCA_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 385 EH2224           THCA_Methylation-20160128_assays 1674.6 Mb
## 386 EH2225               THCA_Methylation-20160128_se    6.1 Mb
## 387  EH955                 THCA_miRNASeqGene-20160128    0.5 Mb
## 388  EH956                     THCA_Mutation-20160128    0.9 Mb
## 389  EH957              THCA_RNASeq2GeneNorm-20160128   30.1 Mb
## 390  EH958                   THCA_RNASeqGene-20160128    0.2 Mb
## 391  EH959                    THCA_RPPAArray-20160128    0.3 Mb
## 392  EH961                       THYM_CNASNP-20160128    0.9 Mb
## 393  EH962                       THYM_CNVSNP-20160128    0.2 Mb
## 394  EH964             THYM_GISTIC_AllByGene-20160128    0.2 Mb
## 395 EH2226                 THYM_GISTIC_Peaks-20160128      0 Mb
## 396  EH965     THYM_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 397 EH2227           THYM_Methylation-20160128_assays  372.2 Mb
## 398 EH2228               THYM_Methylation-20160128_se    6.1 Mb
## 399  EH968                 THYM_miRNASeqGene-20160128    0.1 Mb
## 400  EH969                     THYM_Mutation-20160128    0.2 Mb
## 401  EH970              THYM_RNASeq2GeneNorm-20160128    6.4 Mb
## 402  EH971                    THYM_RPPAArray-20160128    0.2 Mb
## 403  EH973                       UCEC_CNASeq-20160128    0.3 Mb
## 404  EH974                       UCEC_CNASNP-20160128    5.4 Mb
## 405  EH975                       UCEC_CNVSNP-20160128    1.3 Mb
## 406  EH977             UCEC_GISTIC_AllByGene-20160128    0.7 Mb
## 407 EH2229                 UCEC_GISTIC_Peaks-20160128      0 Mb
## 408  EH978     UCEC_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 409 EH2230  UCEC_Methylation_methyl27-20160128_assays   21.7 Mb
## 410 EH2231      UCEC_Methylation_methyl27-20160128_se    0.4 Mb
## 411 EH2232 UCEC_Methylation_methyl450-20160128_assays   1377 Mb
## 412 EH2233     UCEC_Methylation_methyl450-20160128_se    6.1 Mb
## 413  EH982                 UCEC_miRNASeqGene-20160128    0.4 Mb
## 414  EH983                    UCEC_mRNAArray-20160128    2.6 Mb
## 415  EH984                     UCEC_Mutation-20160128    4.6 Mb
## 416  EH985              UCEC_RNASeq2GeneNorm-20160128   18.4 Mb
## 417  EH986                   UCEC_RNASeqGene-20160128    7.7 Mb
## 418  EH987                    UCEC_RPPAArray-20160128    0.7 Mb
## 419  EH989                        UCS_CNASNP-20160128    0.5 Mb
## 420  EH990                        UCS_CNVSNP-20160128    0.2 Mb
## 421  EH992              UCS_GISTIC_AllByGene-20160128    0.3 Mb
## 422 EH2234                  UCS_GISTIC_Peaks-20160128      0 Mb
## 423  EH993      UCS_GISTIC_ThresholdedByGene-20160128    0.3 Mb
## 424 EH2235            UCS_Methylation-20160128_assays  168.3 Mb
## 425 EH2236                UCS_Methylation-20160128_se    6.1 Mb
## 426  EH996                  UCS_miRNASeqGene-20160128    0.1 Mb
## 427  EH997                      UCS_Mutation-20160128    1.2 Mb
## 428  EH998               UCS_RNASeq2GeneNorm-20160128    3.1 Mb
## 429  EH999                     UCS_RPPAArray-20160128    0.1 Mb
## 430 EH1001                        UVM_CNASeq-20160128    0.1 Mb
## 431 EH1002                        UVM_CNASNP-20160128    0.6 Mb
## 432 EH1003                        UVM_CNVSNP-20160128    0.1 Mb
## 433 EH1005              UVM_GISTIC_AllByGene-20160128    0.3 Mb
## 434 EH2237                  UVM_GISTIC_Peaks-20160128      0 Mb
## 435 EH1006      UVM_GISTIC_ThresholdedByGene-20160128    0.2 Mb
## 436 EH2238            UVM_Methylation-20160128_assays  236.4 Mb
## 437 EH2239                UVM_Methylation-20160128_se    6.1 Mb
## 438 EH1009                  UVM_miRNASeqGene-20160128    0.1 Mb
## 439 EH1010                      UVM_Mutation-20160128    0.9 Mb
## 440 EH1011               UVM_RNASeq2GeneNorm-20160128      4 Mb
## 441 EH1012                     UVM_RPPAArray-20160128      0 Mb
##                     rdataclass rdatadateadded rdatadateremoved
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## 140 RangedSummarizedExperiment     2019-01-09             <NA>
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## 147       SummarizedExperiment     2017-10-10             <NA>
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## 151 RangedSummarizedExperiment     2019-01-09             <NA>
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## 153       SummarizedExperiment     2019-01-09             <NA>
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## 157       SummarizedExperiment     2017-10-10             <NA>
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## 166 RangedSummarizedExperiment     2019-01-09             <NA>
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## 168       SummarizedExperiment     2019-01-09             <NA>
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## 206 RangedSummarizedExperiment     2019-01-09             <NA>
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## 213       SummarizedExperiment     2017-10-10             <NA>
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## 219 RangedSummarizedExperiment     2019-01-09             <NA>
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## 221       SummarizedExperiment     2019-01-09             <NA>
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## 225       SummarizedExperiment     2017-10-10             <NA>
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## 235 RangedSummarizedExperiment     2019-01-09             <NA>
## 236       SummarizedExperiment     2017-10-10             <NA>
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## 238       SummarizedExperiment     2019-01-09             <NA>
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## 240       SummarizedExperiment     2019-01-09             <NA>
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## 242       SummarizedExperiment     2017-10-10             <NA>
## 243       SummarizedExperiment     2017-10-10             <NA>
## 244       SummarizedExperiment     2017-10-10             <NA>
## 245           RaggedExperiment     2017-10-10             <NA>
## 246       SummarizedExperiment     2017-10-10             <NA>
## 247       SummarizedExperiment     2017-10-10             <NA>
## 248       SummarizedExperiment     2017-10-10             <NA>
## 249           RaggedExperiment     2017-10-10             <NA>
## 250           RaggedExperiment     2017-10-10             <NA>
## 251       SummarizedExperiment     2017-10-10             <NA>
## 252 RangedSummarizedExperiment     2019-01-09             <NA>
## 253       SummarizedExperiment     2017-10-10             <NA>
## 254       SummarizedExperiment     2019-01-09             <NA>
## 255       SummarizedExperiment     2019-01-09             <NA>
## 256       SummarizedExperiment     2017-10-10             <NA>
## 257       SummarizedExperiment     2017-10-10             <NA>
## 258       SummarizedExperiment     2017-10-10             <NA>
## 259           RaggedExperiment     2017-10-10             <NA>
## 260           RaggedExperiment     2017-10-10             <NA>
## 261           RaggedExperiment     2017-10-10             <NA>
## 262           RaggedExperiment     2017-10-10             <NA>
## 263       SummarizedExperiment     2017-10-10             <NA>
## 264 RangedSummarizedExperiment     2019-01-09             <NA>
## 265       SummarizedExperiment     2017-10-10             <NA>
## 266       SummarizedExperiment     2019-01-09             <NA>
## 267       SummarizedExperiment     2019-01-09             <NA>
## 268       SummarizedExperiment     2019-01-09             <NA>
## 269       SummarizedExperiment     2019-01-09             <NA>
## 270       SummarizedExperiment     2017-10-10             <NA>
## 271       SummarizedExperiment     2017-10-10             <NA>
## 272       SummarizedExperiment     2017-10-10             <NA>
## 273       SummarizedExperiment     2019-01-09             <NA>
## 274       SummarizedExperiment     2017-10-10             <NA>
## 275       SummarizedExperiment     2017-10-10             <NA>
## 276           RaggedExperiment     2017-10-10             <NA>
## 277       SummarizedExperiment     2017-10-10             <NA>
## 278       SummarizedExperiment     2017-10-10             <NA>
## 279       SummarizedExperiment     2017-10-10             <NA>
## 280           RaggedExperiment     2017-10-10             <NA>
## 281           RaggedExperiment     2017-10-10             <NA>
## 282       SummarizedExperiment     2017-10-10             <NA>
## 283 RangedSummarizedExperiment     2019-01-09             <NA>
## 284       SummarizedExperiment     2017-10-10             <NA>
## 285       SummarizedExperiment     2019-01-09             <NA>
## 286           RaggedExperiment     2019-01-09             <NA>
## 287       SummarizedExperiment     2017-10-10             <NA>
## 288           RaggedExperiment     2017-10-10             <NA>
## 289       SummarizedExperiment     2017-10-10             <NA>
## 290       SummarizedExperiment     2017-10-10             <NA>
## 291           RaggedExperiment     2017-10-10             <NA>
## 292           RaggedExperiment     2017-10-10             <NA>
## 293       SummarizedExperiment     2017-10-10             <NA>
## 294 RangedSummarizedExperiment     2019-01-09             <NA>
## 295       SummarizedExperiment     2017-10-10             <NA>
## 296       SummarizedExperiment     2019-01-09             <NA>
## 297           RaggedExperiment     2019-01-09             <NA>
## 298       SummarizedExperiment     2017-10-10             <NA>
## 299           RaggedExperiment     2017-10-10             <NA>
## 300       SummarizedExperiment     2017-10-10             <NA>
## 301       SummarizedExperiment     2017-10-10             <NA>
## 302           RaggedExperiment     2017-10-10             <NA>
## 303           RaggedExperiment     2017-10-10             <NA>
## 304           RaggedExperiment     2017-10-10             <NA>
## 305       SummarizedExperiment     2017-10-10             <NA>
## 306 RangedSummarizedExperiment     2019-01-09             <NA>
## 307       SummarizedExperiment     2017-10-10             <NA>
## 308       SummarizedExperiment     2019-01-09             <NA>
## 309           RaggedExperiment     2019-01-09             <NA>
## 310       SummarizedExperiment     2017-10-10             <NA>
## 311           RaggedExperiment     2017-10-10             <NA>
## 312       SummarizedExperiment     2017-10-10             <NA>
## 313       SummarizedExperiment     2017-10-10             <NA>
## 314           RaggedExperiment     2017-10-10             <NA>
## 315           RaggedExperiment     2017-10-10             <NA>
## 316           RaggedExperiment     2017-10-10             <NA>
## 317       SummarizedExperiment     2017-10-10             <NA>
## 318 RangedSummarizedExperiment     2019-01-09             <NA>
## 319       SummarizedExperiment     2017-10-10             <NA>
## 320       SummarizedExperiment     2019-01-09             <NA>
## 321       SummarizedExperiment     2019-01-09             <NA>
## 322           RaggedExperiment     2019-01-09             <NA>
## 323       SummarizedExperiment     2019-01-09             <NA>
## 324       SummarizedExperiment     2017-10-10             <NA>
## 325       SummarizedExperiment     2017-10-10             <NA>
## 326           RaggedExperiment     2017-10-10             <NA>
## 327       SummarizedExperiment     2017-10-10             <NA>
## 328       SummarizedExperiment     2017-10-10             <NA>
## 329       SummarizedExperiment     2017-10-10             <NA>
## 330           RaggedExperiment     2017-10-10             <NA>
## 331           RaggedExperiment     2017-10-10             <NA>
## 332       SummarizedExperiment     2017-10-10             <NA>
## 333 RangedSummarizedExperiment     2019-01-09             <NA>
## 334       SummarizedExperiment     2017-10-10             <NA>
## 335       SummarizedExperiment     2019-01-09             <NA>
## 336           RaggedExperiment     2019-01-09             <NA>
## 337       SummarizedExperiment     2017-10-10             <NA>
## 338           RaggedExperiment     2017-10-10             <NA>
## 339       SummarizedExperiment     2017-10-10             <NA>
## 340       SummarizedExperiment     2017-10-10             <NA>
## 341           RaggedExperiment     2017-10-16             <NA>
## 342           RaggedExperiment     2017-10-16             <NA>
## 343           RaggedExperiment     2017-10-16             <NA>
## 344       SummarizedExperiment     2019-04-29             <NA>
## 345 RangedSummarizedExperiment     2019-04-29             <NA>
## 346       SummarizedExperiment     2019-04-29             <NA>
## 347       SummarizedExperiment     2019-01-09             <NA>
## 348           RaggedExperiment     2019-01-09             <NA>
## 349       SummarizedExperiment     2017-10-16             <NA>
## 350           RaggedExperiment     2017-10-16             <NA>
## 351       SummarizedExperiment     2017-10-16             <NA>
## 352       SummarizedExperiment     2017-10-16             <NA>
## 353           RaggedExperiment     2017-10-10             <NA>
## 354           RaggedExperiment     2017-10-10             <NA>
## 355           RaggedExperiment     2017-10-10             <NA>
## 356       SummarizedExperiment     2017-10-10             <NA>
## 357 RangedSummarizedExperiment     2019-01-09             <NA>
## 358       SummarizedExperiment     2017-10-10             <NA>
## 359       SummarizedExperiment     2019-01-09             <NA>
## 360           RaggedExperiment     2019-01-09             <NA>
## 361       SummarizedExperiment     2019-01-09             <NA>
## 362       SummarizedExperiment     2019-01-09             <NA>
## 363       SummarizedExperiment     2017-10-10             <NA>
## 364           RaggedExperiment     2017-10-10             <NA>
## 365       SummarizedExperiment     2017-10-10             <NA>
## 366       SummarizedExperiment     2017-10-10             <NA>
## 367       SummarizedExperiment     2017-10-10             <NA>
## 368           RaggedExperiment     2017-10-10             <NA>
## 369           RaggedExperiment     2017-10-10             <NA>
## 370       SummarizedExperiment     2017-10-10             <NA>
## 371 RangedSummarizedExperiment     2019-01-09             <NA>
## 372       SummarizedExperiment     2017-10-10             <NA>
## 373       SummarizedExperiment     2019-01-09             <NA>
## 374           RaggedExperiment     2019-01-09             <NA>
## 375       SummarizedExperiment     2017-10-10             <NA>
## 376           RaggedExperiment     2017-10-10             <NA>
## 377       SummarizedExperiment     2017-10-10             <NA>
## 378       SummarizedExperiment     2017-10-10             <NA>
## 379           RaggedExperiment     2017-10-10             <NA>
## 380           RaggedExperiment     2017-10-10             <NA>
## 381           RaggedExperiment     2017-10-10             <NA>
## 382       SummarizedExperiment     2017-10-10             <NA>
## 383 RangedSummarizedExperiment     2019-01-09             <NA>
## 384       SummarizedExperiment     2017-10-10             <NA>
## 385       SummarizedExperiment     2019-01-09             <NA>
## 386           RaggedExperiment     2019-01-09             <NA>
## 387       SummarizedExperiment     2017-10-10             <NA>
## 388           RaggedExperiment     2017-10-10             <NA>
## 389       SummarizedExperiment     2017-10-10             <NA>
## 390       SummarizedExperiment     2017-10-10             <NA>
## 391       SummarizedExperiment     2017-10-10             <NA>
## 392           RaggedExperiment     2017-10-10             <NA>
## 393           RaggedExperiment     2017-10-10             <NA>
## 394       SummarizedExperiment     2017-10-10             <NA>
## 395 RangedSummarizedExperiment     2019-01-09             <NA>
## 396       SummarizedExperiment     2017-10-10             <NA>
## 397       SummarizedExperiment     2019-01-09             <NA>
## 398           RaggedExperiment     2019-01-09             <NA>
## 399       SummarizedExperiment     2017-10-10             <NA>
## 400           RaggedExperiment     2017-10-10             <NA>
## 401       SummarizedExperiment     2017-10-10             <NA>
## 402       SummarizedExperiment     2017-10-10             <NA>
## 403           RaggedExperiment     2017-10-10             <NA>
## 404           RaggedExperiment     2017-10-10             <NA>
## 405           RaggedExperiment     2017-10-10             <NA>
## 406       SummarizedExperiment     2017-10-10             <NA>
## 407 RangedSummarizedExperiment     2019-01-09             <NA>
## 408       SummarizedExperiment     2017-10-10             <NA>
## 409       SummarizedExperiment     2019-01-09             <NA>
## 410       SummarizedExperiment     2019-01-09             <NA>
## 411           RaggedExperiment     2019-01-09             <NA>
## 412       SummarizedExperiment     2019-01-09             <NA>
## 413       SummarizedExperiment     2017-10-10             <NA>
## 414       SummarizedExperiment     2017-10-10             <NA>
## 415           RaggedExperiment     2017-10-10             <NA>
## 416       SummarizedExperiment     2017-10-10             <NA>
## 417       SummarizedExperiment     2017-10-10             <NA>
## 418       SummarizedExperiment     2017-10-10             <NA>
## 419           RaggedExperiment     2017-10-10             <NA>
## 420           RaggedExperiment     2017-10-10             <NA>
## 421       SummarizedExperiment     2017-10-10             <NA>
## 422 RangedSummarizedExperiment     2019-01-09             <NA>
## 423       SummarizedExperiment     2017-10-10             <NA>
## 424       SummarizedExperiment     2019-01-09             <NA>
## 425           RaggedExperiment     2019-01-09             <NA>
## 426       SummarizedExperiment     2017-10-10             <NA>
## 427           RaggedExperiment     2017-10-10             <NA>
## 428       SummarizedExperiment     2017-10-10             <NA>
## 429       SummarizedExperiment     2017-10-10             <NA>
## 430           RaggedExperiment     2017-10-10             <NA>
## 431           RaggedExperiment     2017-10-10             <NA>
## 432           RaggedExperiment     2017-10-10             <NA>
## 433       SummarizedExperiment     2017-10-10             <NA>
## 434 RangedSummarizedExperiment     2019-01-09             <NA>
## 435       SummarizedExperiment     2017-10-10             <NA>
## 436       SummarizedExperiment     2019-01-09             <NA>
## 437           RaggedExperiment     2019-01-09             <NA>
## 438       SummarizedExperiment     2017-10-10             <NA>
## 439           RaggedExperiment     2017-10-10             <NA>
## 440       SummarizedExperiment     2017-10-10             <NA>
## 441       SummarizedExperiment     2017-10-10             <NA>

Check potential files to be downloaded:

curatedTCGAData(diseaseCode = "COAD", assays = "RPPA*", dry.run = TRUE)
## snapshotDate(): 2020-09-14
## See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
##   ah_id                   title file_size           rdataclass rdatadateadded
## 1 EH639 COAD_RPPAArray-20160128    0.6 Mb SummarizedExperiment     2017-10-10
##   rdatadateremoved
## 1             <NA>

3 Caveats for working with TCGA data

Not all TCGA samples are cancer, there are a mix of samples in each of the 33 cancer types. Use sampleTables on the MultiAssayExperiment object along with data(sampleTypes, package = "TCGAutils") to see what samples are present in the data. There may be tumors that were used to create multiple contributions leading to technical replicates. These should be resolved using the appropriate helper functions such as mergeReplicates. Primary tumors should be selected using TCGAutils::TCGAsampleSelect and used as input to the subsetting mechanisms. See the “Samples in Assays” section of this vignette.

3.1 ACC dataset example

(accmae <- curatedTCGAData("ACC", c("CN*", "Mutation"), FALSE))
## A MultiAssayExperiment object of 3 listed
##  experiments with user-defined names and respective classes.
##  Containing an ExperimentList class object of length 3:
##  [1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 180 columns
##  [2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 180 columns
##  [3] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
## Functionality:
##  experiments() - obtain the ExperimentList instance
##  colData() - the primary/phenotype DataFrame
##  sampleMap() - the sample coordination DataFrame
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment
##  *Format() - convert into a long or wide DataFrame
##  assays() - convert ExperimentList to a SimpleList of matrices
##  exportClass() - save all data to files

Note. For more on how to use a MultiAssayExperiment please see the MultiAssayExperiment vignette.

3.1.1 Subtype information

Some cancer datasets contain associated subtype information within the clinical datasets provided. This subtype information is included in the metadata of colData of the MultiAssayExperiment object. To obtain these variable names, use the getSubtypeMap function from TCGA utils:

head(getSubtypeMap(accmae))
##         ACC_annotations   ACC_subtype
## 1            Patient_ID     patientID
## 2 histological_subtypes     Histology
## 3         mrna_subtypes       C1A/C1B
## 4         mrna_subtypes       mRNA_K4
## 5                  cimp    MethyLevel
## 6     microrna_subtypes miRNA cluster

3.1.2 Typical clinical variables

Another helper function provided by TCGAutils allows users to obtain a set of consistent clinical variable names across several cancer types. Use the getClinicalNames function to obtain a character vector of common clinical variables such as vital status, years to birth, days to death, etc.

head(getClinicalNames("ACC"))
## [1] "years_to_birth"        "vital_status"          "days_to_death"        
## [4] "days_to_last_followup" "tumor_tissue_site"     "pathologic_stage"
colData(accmae)[, getClinicalNames("ACC")][1:5, 1:5]
## DataFrame with 5 rows and 5 columns
##              years_to_birth vital_status days_to_death days_to_last_followup
##                   <integer>    <integer>     <integer>             <integer>
## TCGA-OR-A5J1             58            1          1355                    NA
## TCGA-OR-A5J2             44            1          1677                    NA
## TCGA-OR-A5J3             23            0            NA                  2091
## TCGA-OR-A5J4             23            1           423                    NA
## TCGA-OR-A5J5             30            1           365                    NA
##              tumor_tissue_site
##                    <character>
## TCGA-OR-A5J1           adrenal
## TCGA-OR-A5J2           adrenal
## TCGA-OR-A5J3           adrenal
## TCGA-OR-A5J4           adrenal
## TCGA-OR-A5J5           adrenal

3.1.3 Samples in Assays

The sampleTables function gives an overview of sample types / codes present in the data:

sampleTables(accmae)
## $`ACC_CNASNP-20160128`
## 
## 01 10 11 
## 90 85  5 
## 
## $`ACC_CNVSNP-20160128`
## 
## 01 10 11 
## 90 85  5 
## 
## $`ACC_Mutation-20160128`
## 
## 01 
## 90

Often, an analysis is performed comparing two groups of samples to each other. To facilitate the separation of samples, the splitAssays TCGAutils function identifies all sample types in the assays and moves each into its own assay. By default, all discoverable sample types are separated into a separate experiment. In this case we requested only solid tumors and blood derived normal samples as seen in the sampleTypes reference dataset:

sampleTypes[sampleTypes[["Code"]] %in% c("01", "10"), ]
##    Code           Definition Short.Letter.Code
## 1    01  Primary Solid Tumor                TP
## 10   10 Blood Derived Normal                NB
splitAssays(accmae, c("01", "10"))
## Warning: Some 'sampleCodes' not found in assays
## A MultiAssayExperiment object of 5 listed
##  experiments with user-defined names and respective classes.
##  Containing an ExperimentList class object of length 5:
##  [1] 01_ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 90 columns
##  [2] 10_ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 85 columns
##  [3] 01_ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 90 columns
##  [4] 10_ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 85 columns
##  [5] 01_ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
## Functionality:
##  experiments() - obtain the ExperimentList instance
##  colData() - the primary/phenotype DataFrame
##  sampleMap() - the sample coordination DataFrame
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment
##  *Format() - convert into a long or wide DataFrame
##  assays() - convert ExperimentList to a SimpleList of matrices
##  exportClass() - save all data to files

To obtain a logical vector that could be used for subsetting a MultiAsssayExperiment, refer to TCGAsampleSelect. To select only primary tumors, use the function on the colnames of the MultiAssayExperiment:

tums <- TCGAsampleSelect(colnames(accmae), "01")

You can subsequently provide this input to the subsetting function to select only primary tumors:

accmae[, tums, ]
## harmonizing input:
##   removing 180 sampleMap rows with 'colname' not in colnames of experiments
## A MultiAssayExperiment object of 3 listed
##  experiments with user-defined names and respective classes.
##  Containing an ExperimentList class object of length 3:
##  [1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 90 columns
##  [2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 90 columns
##  [3] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
## Functionality:
##  experiments() - obtain the ExperimentList instance
##  colData() - the primary/phenotype DataFrame
##  sampleMap() - the sample coordination DataFrame
##  `$`, `[`, `[[` - extract colData columns, subset, or experiment
##  *Format() - convert into a long or wide DataFrame
##  assays() - convert ExperimentList to a SimpleList of matrices
##  exportClass() - save all data to files

3.2 Exporting Data

MultiAssayExperiment provides users with an integrative representation of multi-omic TCGA data at the convenience of the user. For those users who wish to use alternative environments, we have provided an export function to extract all the data from a MultiAssayExperiment instance and write them to a series of files:

td <- tempdir()
tempd <- file.path(td, "ACCMAE")
if (!dir.exists(tempd))
    dir.create(tempd)

exportClass(accmae, dir = tempd, fmt = "csv", ext = ".csv")
## Writing about 7 files to disk...
## [1] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_META_0.csv"               
## [2] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_META_1.csv"               
## [3] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_ACC_CNASNP-20160128.csv"  
## [4] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_ACC_CNVSNP-20160128.csv"  
## [5] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_ACC_Mutation-20160128.csv"
## [6] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_colData.csv"              
## [7] "/tmp/RtmpKU4Yy6/ACCMAE/accmae_sampleMap.csv"

This works for all data classes stored (e.g., RaggedExperiment, HDF5Matrix, SummarizedExperiment) in the MultiAssayExperiment via the assays method which converts classes to matrix format (using individual assay methods).

4 Session Information

sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] RaggedExperiment_1.13.0     TCGAutils_1.9.5            
##  [3] curatedTCGAData_1.11.2      MultiAssayExperiment_1.15.4
##  [5] SummarizedExperiment_1.19.6 DelayedArray_0.15.7        
##  [7] matrixStats_0.56.0          Matrix_1.2-18              
##  [9] Biobase_2.49.1              GenomicRanges_1.41.6       
## [11] GenomeInfoDb_1.25.11        IRanges_2.23.10            
## [13] S4Vectors_0.27.12           BiocGenerics_0.35.4        
## [15] BiocStyle_2.17.0           
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.2                    bit64_4.0.5                  
##  [3] jsonlite_1.7.1                AnnotationHub_2.21.5         
##  [5] shiny_1.5.0                   assertthat_0.2.1             
##  [7] askpass_1.1                   interactiveDisplayBase_1.27.5
##  [9] BiocManager_1.30.10           BiocFileCache_1.13.1         
## [11] blob_1.2.1                    Rsamtools_2.5.3              
## [13] GenomeInfoDbData_1.2.3        progress_1.2.2               
## [15] yaml_2.2.1                    BiocVersion_3.12.0           
## [17] pillar_1.4.6                  RSQLite_2.2.0                
## [19] lattice_0.20-41               glue_1.4.2                   
## [21] digest_0.6.25                 promises_1.1.1               
## [23] XVector_0.29.3                rvest_0.3.6                  
## [25] htmltools_0.5.0               httpuv_1.5.4                 
## [27] XML_3.99-0.5                  pkgconfig_2.0.3              
## [29] biomaRt_2.45.2                bookdown_0.20                
## [31] zlibbioc_1.35.0               purrr_0.3.4                  
## [33] xtable_1.8-4                  later_1.1.0.1                
## [35] BiocParallel_1.23.2           openssl_1.4.2                
## [37] tibble_3.0.3                  generics_0.0.2               
## [39] ellipsis_0.3.1                GenomicFeatures_1.41.3       
## [41] magrittr_1.5                  crayon_1.3.4                 
## [43] mime_0.9                      memoise_1.1.0                
## [45] evaluate_0.14                 xml2_1.3.2                   
## [47] prettyunits_1.1.1             tools_4.0.2                  
## [49] hms_0.5.3                     lifecycle_0.2.0              
## [51] stringr_1.4.0                 Biostrings_2.57.2            
## [53] AnnotationDbi_1.51.3          compiler_4.0.2               
## [55] rlang_0.4.7                   grid_4.0.2                   
## [57] GenomicDataCommons_1.13.0     RCurl_1.98-1.2               
## [59] rappdirs_0.3.1                bitops_1.0-6                 
## [61] rmarkdown_2.3                 ExperimentHub_1.15.3         
## [63] DBI_1.1.0                     curl_4.3                     
## [65] R6_2.4.1                      GenomicAlignments_1.25.3     
## [67] rtracklayer_1.49.5            knitr_1.29                   
## [69] dplyr_1.0.2                   fastmap_1.0.1                
## [71] bit_4.0.4                     readr_1.3.1                  
## [73] stringi_1.5.3                 Rcpp_1.0.5                   
## [75] vctrs_0.3.4                   dbplyr_1.4.4                 
## [77] tidyselect_1.1.0              xfun_0.17