Data are stored in remote Zenodo repo.
This function will help download required data and load it into R.
For datasets bundled with the package (tcga, icgc, pcawg_full,
pcawg_simple), local data is used directly without network access.
Note
The Zenodo repository contains fixed-version data. For the latest Ensembl
gene annotations, use build_annotables() to query BioMart directly.
See also
build_annotables() for live Ensembl BioMart queries.
Examples
# \donttest{
load_data("pcawg_full")
#> donor_unique_id
#> <char>
#> 1: BLCA-US::096b4f32-10c1-4737-a0dd-cae04c54ee33
#> 2: BLCA-US::096b4f32-10c1-4737-a0dd-cae04c54ee33
#> 3: BLCA-US::096b4f32-10c1-4737-a0dd-cae04c54ee33
#> 4: BLCA-US::178b28cd-99c3-48dc-8d09-1ef71b4cee80
#> 5: BLCA-US::178b28cd-99c3-48dc-8d09-1ef71b4cee80
#> ---
#> 7251: UCEC-US::fba80122-d8b2-4d8d-a032-9767e8160f9f
#> 7252: UCEC-US::fba80122-d8b2-4d8d-a032-9767e8160f9f
#> 7253: UCEC-US::ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38
#> 7254: UCEC-US::ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38
#> 7255: UCEC-US::ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38
#> submitter_donor_id icgc_donor_id
#> <char> <char>
#> 1: 096b4f32-10c1-4737-a0dd-cae04c54ee33 DO804
#> 2: 096b4f32-10c1-4737-a0dd-cae04c54ee33 DO804
#> 3: 096b4f32-10c1-4737-a0dd-cae04c54ee33 DO804
#> 4: 178b28cd-99c3-48dc-8d09-1ef71b4cee80 DO555
#> 5: 178b28cd-99c3-48dc-8d09-1ef71b4cee80 DO555
#> ---
#> 7251: fba80122-d8b2-4d8d-a032-9767e8160f9f DO42544
#> 7252: fba80122-d8b2-4d8d-a032-9767e8160f9f DO42544
#> 7253: ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38 DO42432
#> 7254: ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38 DO42432
#> 7255: ffaa98a0-2b69-46dc-aee5-c5c3f2abbc38 DO42432
#> aliquot_id submitter_specimen_id
#> <char> <char>
#> 1: e0fccaf5-925a-41f9-b87c-cd5ee4aecb59 27461a27-26eb-4c2c-9c54-e16fbd32c615
#> 2: 301d6ce3-4099-4c1d-8e50-c04b7ce91450 52f538ef-b05d-4c76-9976-ce6d49158016
#> 3: 22e154de-0e3b-443b-8420-48d68d6c1ce4 52f538ef-b05d-4c76-9976-ce6d49158016
#> 4: c1da8eed-4919-4ba5-a735-3fba476c18a7 cd3cfb26-e66f-408e-81f6-3b61c247c976
#> 5: 4838b5a9-968c-4178-bffb-3fafe1f6dc09 59d6683f-5eb7-493d-8e8e-78b88be2cd70
#> ---
#> 7251: e54b7e44-82a3-4016-bc32-129799097b4c ddd2f9e0-0aa3-425b-9d74-74fcc638cb08
#> 7252: ce5b0ba0-2777-4c92-ac50-483174cc5dca cad6c89d-f722-470b-93bc-e8b24c033f0f
#> 7253: 47f826a1-96ed-4f4d-94e0-49f4460ef44f 2729ed97-f971-4d98-8baa-f99404dd2b9f
#> 7254: 712ba532-fb1a-43fa-a356-b446b509ceb7 8bb3a057-8958-4f62-af81-976da2e92df7
#> 7255: ca81a393-ec7d-4538-a64a-417ed188a320 8bb3a057-8958-4f62-af81-976da2e92df7
#> icgc_specimen_id submitter_sample_id icgc_sample_id
#> <char> <char> <char>
#> 1: SP1682 e0fccaf5-925a-41f9-b87c-cd5ee4aecb59 SA5237
#> 2: SP1677 301d6ce3-4099-4c1d-8e50-c04b7ce91450 SA5195
#> 3: SP1677 22e154de-0e3b-443b-8420-48d68d6c1ce4 SA5213
#> 4: SP1135 c1da8eed-4919-4ba5-a735-3fba476c18a7 SA1598
#> 5: SP1132 4838b5a9-968c-4178-bffb-3fafe1f6dc09 SA1556
#> ---
#> 7251: SP92947 e54b7e44-82a3-4016-bc32-129799097b4c SA462448
#> 7252: SP92955 ce5b0ba0-2777-4c92-ac50-483174cc5dca SA462509
#> 7253: SP92731 47f826a1-96ed-4f4d-94e0-49f4460ef44f SA461078
#> 7254: SP92723 712ba532-fb1a-43fa-a356-b446b509ceb7 SA461016
#> 7255: SP92723 ca81a393-ec7d-4538-a64a-417ed188a320 SA461038
load_data("pcawg_simple")
#> tumour_specimen_aliquot_id normal_specimen_aliquot_id
#> <char> <char>
#> 1: 0009b464-b376-4fbc-8a56-da538269a02f 5ef2ed4d-464e-4a51-95e0-401d9ae7be86
#> 2: 003819bc-c415-4e76-887c-931d60ed39e7 9a1c7950-69c9-4f27-800c-8bd834bc3d08
#> 3: 0040b1b6-b07a-4b6e-90ef-133523eaf412 64d942b9-eb38-4c98-8999-4b682377ee85
#> 4: 00493087-9d9d-40ca-86d5-936f1b951c93 d5dfac45-4aff-481d-9117-807ed47b7b10
#> 5: 00508f2b-36bf-44fc-b66b-97e1f3e40bfa a3cc9015-6131-417c-8b71-e6028a4646bd
#> ---
#> 2579: ff870342-f0d6-4450-8f9c-344c046a0baf 8d6563a5-9777-4b2a-a4ac-00b59e6729ff
#> 2580: ffa976f0-aa60-4867-842e-361afa7d68ac 36021aee-1b89-4d5d-94a8-6b9db44a4448
#> 2581: ffad9288-c622-11e3-bf01-24c6515278c0 ff27bf50-c622-11e3-bf01-24c6515278c0
#> 2582: ffdd4feb-aca3-4104-b1e8-954d705a6450 db3bb39b-a1a6-49af-aae3-7cb489a724e4
#> 2583: ffe4bb51-e98a-41a7-a4e1-c3970386889c 15c19e49-6f79-4a67-ab31-3075f38c8432
#> donor_unique_id submitted_donor_id
#> <char> <char>
#> 1: OV-AU::AOCS-117 AOCS-117
#> 2: PBCA-DE::ICGC_PA107 ICGC_PA107
#> 3: LINC-JP::HX17 HX17
#> 4: LGG-US::fc3b7596-f515-446f-81db-fed0154ca2c5 TCGA-EZ-7264
#> 5: PAEN-AU::ICGC_0498 ICGC_0498
#> ---
#> 2579: PRAD-CA::CPCG0208 CPCG0208
#> 2580: CLLE-ES::151 151
#> 2581: LIRI-JP::RK172 RK172
#> 2582: BLCA-US::cce62116-3dcd-400d-ada0-9839ca02466e TCGA-FT-A3EE
#> 2583: PACA-CA::PCSI_0326 PCSI_0326
#> icgc_donor_id icgc_sample_id icgc_specimen_id submitted_specimen_id
#> <char> <char> <char> <char>
#> 1: DO46416 SA505245 SP101724 AOCS-117-13
#> 2: DO36062 SA413814 SP79365 ICGC_PA107
#> 3: DO45049 SA501385 SP98853 HX17T
#> 4: DO22145 SA262459 SP47708 TCGA-EZ-7264-01A
#> 5: DO48578 SA514933 SP106808 8068611
#> ---
#> 2579: DO51079 SA530530 SP112845 CPCG0208-F1
#> 2580: DO52704 SA542175 SP116740 151-02-8TD
#> 2581: DO23552 SA270468 SP50185 RK172_C01
#> 2582: DO720 SA4138 SP1491 TCGA-FT-A3EE-01A
#> 2583: DO51503 SA533736 SP125738 PCSI_0326_Pa_P_526
#> submitted_sample_id tcga_specimen_uuid
#> <char> <char>
#> 1: AOCS-117-3-3 <NA>
#> 2: ICGC_PA107 <NA>
#> 3: HX17T <NA>
#> 4: TCGA-EZ-7264-01A-11D-2024-08 eecba415-5517-4265-8944-07aacbc679fb
#> 5: 8068611 <NA>
#> ---
#> 2579: CPCG0208-F1 <NA>
#> 2580: 151-02-8TD <NA>
#> 2581: RK172_C01 <NA>
#> 2582: TCGA-FT-A3EE-01A-11D-A202-08 2356f78c-0653-468f-83db-6cf6107bd259
#> 2583: PCSI_0326_Pa_P_526 <NA>
#> tcga_sample_uuid tcga_donor_uuid
#> <char> <char>
#> 1: <NA> <NA>
#> 2: <NA> <NA>
#> 3: <NA> <NA>
#> 4: 00493087-9d9d-40ca-86d5-936f1b951c93 fc3b7596-f515-446f-81db-fed0154ca2c5
#> 5: <NA> <NA>
#> ---
#> 2579: <NA> <NA>
#> 2580: <NA> <NA>
#> 2581: <NA> <NA>
#> 2582: ffdd4feb-aca3-4104-b1e8-954d705a6450 cce62116-3dcd-400d-ada0-9839ca02466e
#> 2583: <NA> <NA>
load_data("tcga")
#> case_id
#> <char>
#> 1: 30a1fe5e-5b12-472c-aa86-c2db8167ab23
#> 2: 30a1fe5e-5b12-472c-aa86-c2db8167ab23
#> 3: 30a1fe5e-5b12-472c-aa86-c2db8167ab23
#> 4: 30a1fe5e-5b12-472c-aa86-c2db8167ab23
#> 5: 30a1fe5e-5b12-472c-aa86-c2db8167ab23
#> ---
#> 150845: 4756acc0-4e96-44d4-b359-04d64dc7eb84
#> 150846: 4756acc0-4e96-44d4-b359-04d64dc7eb84
#> 150847: 4756acc0-4e96-44d4-b359-04d64dc7eb84
#> 150848: 4756acc0-4e96-44d4-b359-04d64dc7eb84
#> 150849: 4756acc0-4e96-44d4-b359-04d64dc7eb84
#> aliquot_ids submitter_aliquot_ids
#> <char> <char>
#> 1: bab8561e-b84b-4f77-abbd-0053b44a7cb1 TCGA-02-0001-10A-01W-0188-10
#> 2: ffd8c4e1-f515-4406-b2be-19a87b60b295 TCGA-02-0001-01C-01R-0179-07
#> 3: 9b62c8ff-549c-48ae-8893-8bde079acec0 TCGA-02-0001-01C-01R-0676-04
#> 4: f50bd78c-039d-483c-aae6-d56a74e9911e TCGA-02-0001-01C-01D-0888-01
#> 5: baa8958d-ebc9-4df7-83d8-2fc3782ac980 TCGA-02-0001-10A-01W-0190-09
#> ---
#> 150845: 212eae3c-4ad5-48e0-90af-b6fe1dfc5554 TCGA-ZX-AA5X-01A-11R-A42T-07
#> 150846: 13f9434b-5c9f-4767-99f0-5b4528ead4a0 TCGA-ZX-AA5X-10A-01D-A42Q-01
#> 150847: d4539dbc-3874-4649-9dc6-bd27f21581fd TCGA-ZX-AA5X-01A-11R-A42V-13
#> 150848: 6d72c3e1-cb80-4c1d-852f-bb5337af1fdf TCGA-ZX-AA5X-01A-11D-A42P-05
#> 150849: d305bae2-19f6-440c-9eb9-f0395a2b3a2d TCGA-ZX-AA5X-01A-11D-A42N-01
#> submitter_id sample_id
#> <char> <char>
#> 1: TCGA-02-0001 TCGA-02-0001-10
#> 2: TCGA-02-0001 TCGA-02-0001-01
#> 3: TCGA-02-0001 TCGA-02-0001-01
#> 4: TCGA-02-0001 TCGA-02-0001-01
#> 5: TCGA-02-0001 TCGA-02-0001-10
#> ---
#> 150845: TCGA-ZX-AA5X TCGA-ZX-AA5X-01
#> 150846: TCGA-ZX-AA5X TCGA-ZX-AA5X-10
#> 150847: TCGA-ZX-AA5X TCGA-ZX-AA5X-01
#> 150848: TCGA-ZX-AA5X TCGA-ZX-AA5X-01
#> 150849: TCGA-ZX-AA5X TCGA-ZX-AA5X-01
load_data("icgc")
#> icgc_sample_id submitted_sample_id icgc_specimen_id
#> <char> <char> <char>
#> 1: SA170678 TCGA-02-0104-01A-01G-0295-06 SP29019
#> 2: SA170653 TCGA-02-0104-01A-01T-0301-07 SP29019
#> 3: SA170728 TCGA-02-0104-01A-01R-0299-03 SP29019
#> 4: SA170688 TCGA-02-0104-01A-01G-0296-02 SP29019
#> 5: SA170698 TCGA-02-0104-01A-01G-0326-02 SP29019
#> ---
#> 155870: SA539137 TCGA-94-8490-01A-11H-2325-13 SP115145
#> 155871: SA539135 TCGA-94-8490-01A-11D-2323-08 SP115145
#> 155872: SA539140 TCGA-94-8490-10A-01D-2322-01 SP115146
#> 155873: SA539141 TCGA-94-8490-10A-01D-2323-08 SP115146
#> 155874: SA539142 TCGA-94-8490-10A-01W-2345-08 SP115146
#> submitted_specimen_id icgc_donor_id submitted_donor_id
#> <char> <char> <char>
#> 1: TCGA-02-0104-01A DO13695 TCGA-02-0104
#> 2: TCGA-02-0104-01A DO13695 TCGA-02-0104
#> 3: TCGA-02-0104-01A DO13695 TCGA-02-0104
#> 4: TCGA-02-0104-01A DO13695 TCGA-02-0104
#> 5: TCGA-02-0104-01A DO13695 TCGA-02-0104
#> ---
#> 155870: TCGA-94-8490-01A DO52021 TCGA-94-8490
#> 155871: TCGA-94-8490-01A DO52021 TCGA-94-8490
#> 155872: TCGA-94-8490-10A DO52021 TCGA-94-8490
#> 155873: TCGA-94-8490-10A DO52021 TCGA-94-8490
#> 155874: TCGA-94-8490-10A DO52021 TCGA-94-8490
# }