Function restores codes and counts for each cohort from TCGA project.
infoTCGA()
A list with a tabular information from http://gdac.broadinstitute.org/.
If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.
RTCGA website http://rtcga.github.io/RTCGA/articles/Data_Download.html.
Other RTCGA: RTCGA-package,
boxplotTCGA, checkTCGA,
convertTCGA, createTCGA,
datasetsTCGA, downloadTCGA,
expressionsTCGA, heatmapTCGA,
installTCGA, kmTCGA,
mutationsTCGA, pcaTCGA,
readTCGA, survivalTCGA,
theme_RTCGA
infoTCGA()#> Cohort BCR Clinical CN LowP Methylation mRNA mRNASeq miR #> ACC-counts ACC 92 92 90 0 80 0 79 0 #> BLCA-counts BLCA 412 412 410 112 412 0 408 0 #> BRCA-counts BRCA 1098 1097 1089 19 1097 526 1093 0 #> CESC-counts CESC 307 307 295 50 307 0 304 0 #> CHOL-counts CHOL 51 45 36 0 36 0 36 0 #> COAD-counts COAD 460 458 451 69 457 153 457 0 #> COADREAD-counts COADREAD 631 629 616 104 622 222 623 0 #> DLBC-counts DLBC 58 48 48 0 48 0 48 0 #> ESCA-counts ESCA 185 185 184 51 185 0 184 0 #> FPPP-counts FPPP 38 38 0 0 0 0 0 0 #> GBM-counts GBM 613 595 577 0 420 540 160 565 #> GBMLGG-counts GBMLGG 1129 1110 1090 52 936 567 676 565 #> HNSC-counts HNSC 528 528 522 108 528 0 520 0 #> KICH-counts KICH 113 113 66 0 66 0 66 0 #> KIPAN-counts KIPAN 973 941 883 0 892 88 889 0 #> KIRC-counts KIRC 537 537 528 0 535 72 533 0 #> KIRP-counts KIRP 323 291 289 0 291 16 290 0 #> LAML-counts LAML 200 200 197 0 194 0 179 0 #> LGG-counts LGG 516 515 513 52 516 27 516 0 #> LIHC-counts LIHC 377 377 370 0 377 0 371 0 #> LUAD-counts LUAD 585 522 516 120 578 32 515 0 #> LUSC-counts LUSC 504 504 501 0 503 154 501 0 #> MESO-counts MESO 87 87 87 0 87 0 87 0 #> OV-counts OV 602 591 586 0 594 574 304 570 #> PAAD-counts PAAD 185 185 184 0 184 0 178 0 #> PCPG-counts PCPG 179 179 175 0 179 0 179 0 #> PRAD-counts PRAD 499 499 492 115 498 0 497 0 #> READ-counts READ 171 171 165 35 165 69 166 0 #> SARC-counts SARC 261 261 257 0 261 0 259 0 #> SKCM-counts SKCM 470 470 469 118 470 0 469 0 #> STAD-counts STAD 443 443 442 107 443 0 415 0 #> STES-counts STES 628 628 626 158 628 0 599 0 #> TGCT-counts TGCT 150 134 150 0 150 0 150 0 #> THCA-counts THCA 503 503 499 98 503 0 501 0 #> THYM-counts THYM 124 124 123 0 124 0 120 0 #> UCEC-counts UCEC 560 548 540 106 547 54 545 0 #> UCS-counts UCS 57 57 56 0 57 0 57 0 #> UVM-counts UVM 80 80 80 51 80 0 80 0 #> miRSeq RPPA MAF rawMAF #> ACC-counts 80 46 90 0 #> BLCA-counts 409 344 130 395 #> BRCA-counts 1078 887 977 0 #> CESC-counts 307 173 194 0 #> CHOL-counts 36 30 35 0 #> COAD-counts 406 360 154 367 #> COADREAD-counts 549 491 223 489 #> DLBC-counts 47 33 48 0 #> ESCA-counts 184 126 185 0 #> FPPP-counts 23 0 0 0 #> GBM-counts 0 238 290 290 #> GBMLGG-counts 512 668 576 806 #> HNSC-counts 523 212 279 510 #> KICH-counts 66 63 66 66 #> KIPAN-counts 873 756 644 799 #> KIRC-counts 516 478 417 451 #> KIRP-counts 291 215 161 282 #> LAML-counts 188 0 197 0 #> LGG-counts 512 430 286 516 #> LIHC-counts 372 63 198 373 #> LUAD-counts 513 365 230 542 #> LUSC-counts 478 328 178 0 #> MESO-counts 87 63 0 0 #> OV-counts 453 426 316 469 #> PAAD-counts 178 123 150 184 #> PCPG-counts 179 80 179 0 #> PRAD-counts 494 352 332 498 #> READ-counts 143 131 69 122 #> SARC-counts 259 223 247 0 #> SKCM-counts 448 353 343 366 #> STAD-counts 436 357 289 395 #> STES-counts 620 483 474 395 #> TGCT-counts 150 118 149 0 #> THCA-counts 502 222 402 496 #> THYM-counts 124 90 123 0 #> UCEC-counts 538 440 248 0 #> UCS-counts 56 48 57 0 #> UVM-counts 80 12 80 0library(magrittr) (cohorts <- infoTCGA() %>% rownames() %>% sub('-counts', '', x=.))#> [1] "ACC" "BLCA" "BRCA" "CESC" "CHOL" "COAD" #> [7] "COADREAD" "DLBC" "ESCA" "FPPP" "GBM" "GBMLGG" #> [13] "HNSC" "KICH" "KIPAN" "KIRC" "KIRP" "LAML" #> [19] "LGG" "LIHC" "LUAD" "LUSC" "MESO" "OV" #> [25] "PAAD" "PCPG" "PRAD" "READ" "SARC" "SKCM" #> [31] "STAD" "STES" "TGCT" "THCA" "THYM" "UCEC" #> [37] "UCS" "UVM"# in knitr chunk -> results='asis' knitr::kable(infoTCGA())#> #> #> | |Cohort |BCR |Clinical |CN |LowP |Methylation |mRNA |mRNASeq |miR |miRSeq |RPPA |MAF |rawMAF | #> |:---------------|:--------|:----|:--------|:----|:----|:-----------|:----|:-------|:---|:------|:----|:---|:------| #> |ACC-counts |ACC |92 |92 |90 |0 |80 |0 |79 |0 |80 |46 |90 |0 | #> |BLCA-counts |BLCA |412 |412 |410 |112 |412 |0 |408 |0 |409 |344 |130 |395 | #> |BRCA-counts |BRCA |1098 |1097 |1089 |19 |1097 |526 |1093 |0 |1078 |887 |977 |0 | #> |CESC-counts |CESC |307 |307 |295 |50 |307 |0 |304 |0 |307 |173 |194 |0 | #> |CHOL-counts |CHOL |51 |45 |36 |0 |36 |0 |36 |0 |36 |30 |35 |0 | #> |COAD-counts |COAD |460 |458 |451 |69 |457 |153 |457 |0 |406 |360 |154 |367 | #> |COADREAD-counts |COADREAD |631 |629 |616 |104 |622 |222 |623 |0 |549 |491 |223 |489 | #> |DLBC-counts |DLBC |58 |48 |48 |0 |48 |0 |48 |0 |47 |33 |48 |0 | #> |ESCA-counts |ESCA |185 |185 |184 |51 |185 |0 |184 |0 |184 |126 |185 |0 | #> |FPPP-counts |FPPP |38 |38 |0 |0 |0 |0 |0 |0 |23 |0 |0 |0 | #> |GBM-counts |GBM |613 |595 |577 |0 |420 |540 |160 |565 |0 |238 |290 |290 | #> |GBMLGG-counts |GBMLGG |1129 |1110 |1090 |52 |936 |567 |676 |565 |512 |668 |576 |806 | #> |HNSC-counts |HNSC |528 |528 |522 |108 |528 |0 |520 |0 |523 |212 |279 |510 | #> |KICH-counts |KICH |113 |113 |66 |0 |66 |0 |66 |0 |66 |63 |66 |66 | #> |KIPAN-counts |KIPAN |973 |941 |883 |0 |892 |88 |889 |0 |873 |756 |644 |799 | #> |KIRC-counts |KIRC |537 |537 |528 |0 |535 |72 |533 |0 |516 |478 |417 |451 | #> |KIRP-counts |KIRP |323 |291 |289 |0 |291 |16 |290 |0 |291 |215 |161 |282 | #> |LAML-counts |LAML |200 |200 |197 |0 |194 |0 |179 |0 |188 |0 |197 |0 | #> |LGG-counts |LGG |516 |515 |513 |52 |516 |27 |516 |0 |512 |430 |286 |516 | #> |LIHC-counts |LIHC |377 |377 |370 |0 |377 |0 |371 |0 |372 |63 |198 |373 | #> |LUAD-counts |LUAD |585 |522 |516 |120 |578 |32 |515 |0 |513 |365 |230 |542 | #> |LUSC-counts |LUSC |504 |504 |501 |0 |503 |154 |501 |0 |478 |328 |178 |0 | #> |MESO-counts |MESO |87 |87 |87 |0 |87 |0 |87 |0 |87 |63 |0 |0 | #> |OV-counts |OV |602 |591 |586 |0 |594 |574 |304 |570 |453 |426 |316 |469 | #> |PAAD-counts |PAAD |185 |185 |184 |0 |184 |0 |178 |0 |178 |123 |150 |184 | #> |PCPG-counts |PCPG |179 |179 |175 |0 |179 |0 |179 |0 |179 |80 |179 |0 | #> |PRAD-counts |PRAD |499 |499 |492 |115 |498 |0 |497 |0 |494 |352 |332 |498 | #> |READ-counts |READ |171 |171 |165 |35 |165 |69 |166 |0 |143 |131 |69 |122 | #> |SARC-counts |SARC |261 |261 |257 |0 |261 |0 |259 |0 |259 |223 |247 |0 | #> |SKCM-counts |SKCM |470 |470 |469 |118 |470 |0 |469 |0 |448 |353 |343 |366 | #> |STAD-counts |STAD |443 |443 |442 |107 |443 |0 |415 |0 |436 |357 |289 |395 | #> |STES-counts |STES |628 |628 |626 |158 |628 |0 |599 |0 |620 |483 |474 |395 | #> |TGCT-counts |TGCT |150 |134 |150 |0 |150 |0 |150 |0 |150 |118 |149 |0 | #> |THCA-counts |THCA |503 |503 |499 |98 |503 |0 |501 |0 |502 |222 |402 |496 | #> |THYM-counts |THYM |124 |124 |123 |0 |124 |0 |120 |0 |124 |90 |123 |0 | #> |UCEC-counts |UCEC |560 |548 |540 |106 |547 |54 |545 |0 |538 |440 |248 |0 | #> |UCS-counts |UCS |57 |57 |56 |0 |57 |0 |57 |0 |56 |48 |57 |0 | #> |UVM-counts |UVM |80 |80 |80 |51 |80 |0 |80 |0 |80 |12 |80 |0 |