Get available clinical data for samples in a case list
Arguments
- caseList
character(1). Case list identifier (e.g. "ccle_broad_2019_sequenced"). Refer tocaseLists()for details.
Examples
## DLBCL TCGA ====
x <- clinicalData(caseList = "dlbc_tcga_pan_can_atlas_2018_rna_seq_v2_mrna")
print(x)
#> DataFrame with 48 rows and 48 columns
#> age ajccStagingEdition aneuploidyScore
#> <integer> <character> <integer>
#> TCGA_FA_8693_01 75 7TH 0
#> TCGA_FA_A4BB_01 67 7TH 1
#> TCGA_FA_A4XK_01 40 7TH 7
#> TCGA_FA_A6HN_01 73 7TH 0
#> TCGA_FA_A6HO_01 58 7TH 24
#> ... ... ... ...
#> TCGA_GS_A9U4_01 27 7TH 11
#> TCGA_RQ_A68N_01 63 7TH 16
#> TCGA_RQ_A6JB_01 62 7TH 0
#> TCGA_RQ_AAAT_01 63 7TH 13
#> TCGA_VB_A8QN_01 55 7TH 1
#> cancerType cancerTypeAcronym cancerTypeDetailed
#> <character> <character> <character>
#> TCGA_FA_8693_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_FA_A4BB_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_FA_A4XK_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_FA_A6HN_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_FA_A6HO_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> ... ... ... ...
#> TCGA_GS_A9U4_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_RQ_A68N_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_RQ_A6JB_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_RQ_AAAT_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> TCGA_VB_A8QN_01 Mature B-Cell Neopla.. DLBC Diffuse Large B-Cell..
#> daysLastFollowup daysToBirth daysToInitialPathologicDiagnosis
#> <integer> <integer> <integer>
#> TCGA_FA_8693_01 132 -27468 0
#> TCGA_FA_A4BB_01 132 -24590 0
#> TCGA_FA_A4XK_01 456 -14723 0
#> TCGA_FA_A6HN_01 6 -27025 0
#> TCGA_FA_A6HO_01 749 -21330 0
#> ... ... ... ...
#> TCGA_GS_A9U4_01 NA -10075 0
#> TCGA_RQ_A68N_01 788 -23127 0
#> TCGA_RQ_A6JB_01 1 -22859 0
#> TCGA_RQ_AAAT_01 17 -23178 0
#> TCGA_VB_A8QN_01 0 -20270 0
#> dfsMonths dfsStatus dssMonths
#> <numeric> <character> <numeric>
#> TCGA_FA_8693_01 4.33968 0:DiseaseFree 4.33968
#> TCGA_FA_A4BB_01 NA NA 4.33968
#> TCGA_FA_A4XK_01 23.27646 0:DiseaseFree 23.27646
#> TCGA_FA_A6HN_01 NA NA 1.90683
#> TCGA_FA_A6HO_01 24.29562 1:Recurred/Progressed 24.62439
#> ... ... ... ...
#> TCGA_GS_A9U4_01 NA NA 12.8546536
#> TCGA_RQ_A68N_01 NA NA 25.9065654
#> TCGA_RQ_A6JB_01 NA NA 0.0328764
#> TCGA_RQ_AAAT_01 0.558898 0:DiseaseFree 0.5588980
#> TCGA_VB_A8QN_01 NA NA 0.0000000
#> dssStatus ethnicity
#> <character> <character>
#> TCGA_FA_8693_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> TCGA_FA_A4BB_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> TCGA_FA_A4XK_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> TCGA_FA_A6HN_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> TCGA_FA_A6HO_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> ... ... ...
#> TCGA_GS_A9U4_01 1:DEAD WITH TUMOR Hispanic Or Latino
#> TCGA_RQ_A68N_01 0:ALIVE OR DEAD TUMO.. Hispanic Or Latino
#> TCGA_RQ_A6JB_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> TCGA_RQ_AAAT_01 0:ALIVE OR DEAD TUMO.. Hispanic Or Latino
#> TCGA_VB_A8QN_01 0:ALIVE OR DEAD TUMO.. Not Hispanic Or Latino
#> formCompletionDate fractionGenomeAltered
#> <character> <numeric>
#> TCGA_FA_8693_01 9/12/12 0.0105
#> TCGA_FA_A4BB_01 2/11/13 0.0026
#> TCGA_FA_A4XK_01 3/22/13 0.1389
#> TCGA_FA_A6HN_01 10/21/13 0.0545
#> TCGA_FA_A6HO_01 10/21/13 0.2672
#> ... ... ...
#> TCGA_GS_A9U4_01 6/2/14 0.0000
#> TCGA_RQ_A68N_01 12/12/13 0.4525
#> TCGA_RQ_A6JB_01 11/14/14 0.0204
#> TCGA_RQ_AAAT_01 7/28/14 0.2376
#> TCGA_VB_A8QN_01 2/15/15 0.1075
#> historyNeoadjuvantTrtyn icd10 icdO3Histology icdO3Site
#> <character> <character> <character> <character>
#> TCGA_FA_8693_01 No C83.3 9680/3 C16.9
#> TCGA_FA_A4BB_01 No C83.3 9680/3 C77.3
#> TCGA_FA_A4XK_01 No C83.3 9680/3 C17.1
#> TCGA_FA_A6HN_01 No C83.3 9680/3 C77.0
#> TCGA_FA_A6HO_01 No C83.3 9680/3 C77.0
#> ... ... ... ... ...
#> TCGA_GS_A9U4_01 No C83.3 9680/3 C77.0
#> TCGA_RQ_A68N_01 No C71.7 9680/3 C71.7
#> TCGA_RQ_A6JB_01 No C83.3 9680/3 C41.0
#> TCGA_RQ_AAAT_01 No C71.6 9680/3 C71.6
#> TCGA_VB_A8QN_01 No C83.3 9680/3 C16.9
#> inPancanpathwaysFreeze informedConsentVerified msiScoreMantis
#> <character> <character> <numeric>
#> TCGA_FA_8693_01 Yes Yes 0.2840
#> TCGA_FA_A4BB_01 Yes Yes 0.3132
#> TCGA_FA_A4XK_01 Yes Yes 0.3094
#> TCGA_FA_A6HN_01 Yes Yes 0.3199
#> TCGA_FA_A6HO_01 Yes Yes 0.3151
#> ... ... ... ...
#> TCGA_GS_A9U4_01 Yes Yes 0.3297
#> TCGA_RQ_A68N_01 Yes Yes 0.3152
#> TCGA_RQ_A6JB_01 Yes Yes 0.3101
#> TCGA_RQ_AAAT_01 Yes Yes 0.3278
#> TCGA_VB_A8QN_01 Yes Yes 0.3279
#> msiSensorScore mutationCount newTumorEventAfterInitialTreatment
#> <numeric> <integer> <character>
#> TCGA_FA_8693_01 0.01 171 No
#> TCGA_FA_A4BB_01 0.01 92 No
#> TCGA_FA_A4XK_01 0.10 88 NA
#> TCGA_FA_A6HN_01 0.05 163 NA
#> TCGA_FA_A6HO_01 0.01 56 Yes
#> ... ... ... ...
#> TCGA_GS_A9U4_01 0.00 31 Yes
#> TCGA_RQ_A68N_01 0.39 192 No
#> TCGA_RQ_A6JB_01 0.28 99 NA
#> TCGA_RQ_AAAT_01 0.42 173 NA
#> TCGA_VB_A8QN_01 0.06 141 NA
#> oncotreeCode osMonths osStatus otherPatientId
#> <character> <numeric> <character> <character>
#> TCGA_FA_8693_01 DLBCLNOS 4.33968 0:LIVING a43e5f0e-a21f-48d8-9..
#> TCGA_FA_A4BB_01 DLBCLNOS 4.33968 0:LIVING 1843C82E-7A35-474F-9..
#> TCGA_FA_A4XK_01 DLBCLNOS 23.27646 1:DECEASED A5B188F0-A6D3-4D4A-B..
#> TCGA_FA_A6HN_01 DLBCLNOS 1.90683 1:DECEASED 0BF573AC-CD1E-42D8-9..
#> TCGA_FA_A6HO_01 DLBCLNOS 24.62439 0:LIVING 69F23725-ADCA-48AC-9..
#> ... ... ... ... ...
#> TCGA_GS_A9U4_01 DLBCLNOS 12.8546536 1:DECEASED 0E251C03-BF86-4ED8-B..
#> TCGA_RQ_A68N_01 DLBCLNOS 25.9065654 0:LIVING 25FF86AF-BEB4-480C-B..
#> TCGA_RQ_A6JB_01 DLBCLNOS 0.0328764 0:LIVING DC87A809-95DE-4EB7-A..
#> TCGA_RQ_AAAT_01 DLBCLNOS 0.5588980 0:LIVING 4DD86EBD-EF16-4B2B-9..
#> TCGA_VB_A8QN_01 DLBCLNOS 0.0000000 0:LIVING A6923479-4E68-4EA8-8..
#> personNeoplasmCancerStatus pfsMonths pfsStatus priorDx
#> <character> <numeric> <character> <character>
#> TCGA_FA_8693_01 Tumor Free 4.33968 0:CENSORED No
#> TCGA_FA_A4BB_01 With Tumor 4.33968 0:CENSORED No
#> TCGA_FA_A4XK_01 Tumor Free 23.27646 0:CENSORED No
#> TCGA_FA_A6HN_01 Tumor Free 1.90683 0:CENSORED No
#> TCGA_FA_A6HO_01 Tumor Free 24.29562 1:PROGRESSION No
#> ... ... ... ... ...
#> TCGA_GS_A9U4_01 With Tumor 3.4848933 1:PROGRESSION No
#> TCGA_RQ_A68N_01 Tumor Free 25.9065654 0:CENSORED No
#> TCGA_RQ_A6JB_01 NA 0.0328764 0:CENSORED No
#> TCGA_RQ_AAAT_01 Tumor Free 0.5588980 0:CENSORED No
#> TCGA_VB_A8QN_01 NA 0.0000000 0:CENSORED No
#> race radiationTherapy sampleCount sampleType
#> <character> <character> <integer> <character>
#> TCGA_FA_8693_01 White No 1 Primary
#> TCGA_FA_A4BB_01 White No 1 Primary
#> TCGA_FA_A4XK_01 Asian No 1 Primary
#> TCGA_FA_A6HN_01 Asian No 1 Primary
#> TCGA_FA_A6HO_01 Asian No 1 Primary
#> ... ... ... ... ...
#> TCGA_GS_A9U4_01 White No 1 Primary
#> TCGA_RQ_A68N_01 White No 1 Primary
#> TCGA_RQ_A6JB_01 White NA 1 Primary
#> TCGA_RQ_AAAT_01 White NA 1 Primary
#> TCGA_VB_A8QN_01 White No 1 Primary
#> sex somaticStatus subtype
#> <character> <character> <character>
#> TCGA_FA_8693_01 Male Matched DLBC
#> TCGA_FA_A4BB_01 Male Matched DLBC
#> TCGA_FA_A4XK_01 Male Matched DLBC
#> TCGA_FA_A6HN_01 Male Matched DLBC
#> TCGA_FA_A6HO_01 Female Matched DLBC
#> ... ... ... ...
#> TCGA_GS_A9U4_01 Female Matched DLBC
#> TCGA_RQ_A68N_01 Male Matched DLBC
#> TCGA_RQ_A6JB_01 Female Matched DLBC
#> TCGA_RQ_AAAT_01 Female Matched DLBC
#> TCGA_VB_A8QN_01 Male Matched DLBC
#> tissueProspectiveCollectionIndicator
#> <character>
#> TCGA_FA_8693_01 Yes
#> TCGA_FA_A4BB_01 Yes
#> TCGA_FA_A4XK_01 Yes
#> TCGA_FA_A6HN_01 Yes
#> TCGA_FA_A6HO_01 Yes
#> ... ...
#> TCGA_GS_A9U4_01 No
#> TCGA_RQ_A68N_01 No
#> TCGA_RQ_A6JB_01 No
#> TCGA_RQ_AAAT_01 No
#> TCGA_VB_A8QN_01 Yes
#> tissueRetrospectiveCollectionIndicator tissueSourceSite
#> <character> <character>
#> TCGA_FA_8693_01 No Asterand
#> TCGA_FA_A4BB_01 No Asterand
#> TCGA_FA_A4XK_01 No Asterand
#> TCGA_FA_A6HN_01 No Asterand
#> TCGA_FA_A6HO_01 No Asterand
#> ... ... ...
#> TCGA_GS_A9U4_01 Yes Fundacio Clinic per ..
#> TCGA_RQ_A68N_01 Yes St. Joseph's Hospita..
#> TCGA_RQ_A6JB_01 Yes St. Joseph's Hospita..
#> TCGA_RQ_AAAT_01 Yes St. Joseph's Hospita..
#> TCGA_VB_A8QN_01 No Global BioClinical -..
#> tissueSourceSiteCode tmbNonsynonymous tumorType
#> <character> <numeric> <character>
#> TCGA_FA_8693_01 FA 5.56667 Diffuse Large B-Cell..
#> TCGA_FA_A4BB_01 FA 3.06667 Diffuse Large B-Cell..
#> TCGA_FA_A4XK_01 FA 2.93333 Diffuse Large B-Cell..
#> TCGA_FA_A6HN_01 FA 5.50000 Diffuse Large B-Cell..
#> TCGA_FA_A6HO_01 FA 1.86667 Diffuse Large B-Cell..
#> ... ... ... ...
#> TCGA_GS_A9U4_01 GS 1.06667 Diffuse Large B-Cell..
#> TCGA_RQ_A68N_01 RQ 6.36667 CNS, Primary Diffuse..
#> TCGA_RQ_A6JB_01 RQ 3.33333 CNS, Primary Diffuse..
#> TCGA_RQ_AAAT_01 RQ 5.73333 CNS, Primary Diffuse..
#> TCGA_VB_A8QN_01 VB 4.73333 Diffuse Large B-Cell..
#> weight
#> <numeric>
#> TCGA_FA_8693_01 82
#> TCGA_FA_A4BB_01 85
#> TCGA_FA_A4XK_01 60
#> TCGA_FA_A6HN_01 58
#> TCGA_FA_A6HO_01 61
#> ... ...
#> TCGA_GS_A9U4_01 50.0
#> TCGA_RQ_A68N_01 58.0
#> TCGA_RQ_A6JB_01 72.0
#> TCGA_RQ_AAAT_01 68.2
#> TCGA_VB_A8QN_01 75.0
## CCLE Broad 2019 ====
x <- clinicalData(caseList = "ccle_broad_2019_sequenced")
print(x)
#> DataFrame with 1570 rows and 43 columns
#> age annotationSource
#> <numeric> <character>
#> A101D_SKIN 56 CCLE
#> A1207_CENTRAL_NERVOUS_SYSTEM NA ACHILLES
#> A172_CENTRAL_NERVOUS_SYSTEM 53 CCLE
#> A204_SOFT_TISSUE 1 CCLE
#> A2058_SKIN 43 CCLE
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA CCLE
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST 63 CCLE
#> ZR7530_BREAST 47 CCLE
#> cancerType
#> <character>
#> A101D_SKIN Melanoma
#> A1207_CENTRAL_NERVOUS_SYSTEM Glioma
#> A172_CENTRAL_NERVOUS_SYSTEM Glioma
#> A204_SOFT_TISSUE Soft Tissue Sarcoma
#> A2058_SKIN Melanoma
#> ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM Glioma
#> YMB1E_BREAST Cancer of Unknown Pr..
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE Cancer of Unknown Pr..
#> ZR751_BREAST Breast Cancer
#> ZR7530_BREAST Breast Cancer
#> cancerTypeDetailed cellLineSource
#> <character> <character>
#> A101D_SKIN Cutaneous Melanoma GNF
#> A1207_CENTRAL_NERVOUS_SYSTEM Glioblastoma Multifo.. NA
#> A172_CENTRAL_NERVOUS_SYSTEM Glioblastoma Multifo.. ATCC
#> A204_SOFT_TISSUE Embryonal Rhabdomyos.. NIBRI
#> A2058_SKIN Cutaneous Melanoma GNF
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM Glioblastoma Multifo.. GNF
#> YMB1E_BREAST Cancer of Unknown Pr.. NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE Cancer of Unknown Pr.. NA
#> ZR751_BREAST Chondrosarcoma ATCC
#> ZR7530_BREAST Invasive Breast Carc.. GNF
#> characteristics depmapid
#> <character> <character>
#> A101D_SKIN NA ACH-000008
#> A1207_CENTRAL_NERVOUS_SYSTEM NA ACH-000283
#> A172_CENTRAL_NERVOUS_SYSTEM Adherent ACH-000558
#> A204_SOFT_TISSUE NA ACH-000201
#> A2058_SKIN NA ACH-000788
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA ACH-000570
#> YMB1E_BREAST NA ACH-002208
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA ACH-002317
#> ZR751_BREAST adherent epithelial ACH-000097
#> ZR7530_BREAST NA ACH-000828
#> diseaseOntology doublingTime
#> <character> <numeric>
#> A101D_SKIN NA 69.1
#> A1207_CENTRAL_NERVOUS_SYSTEM NA NA
#> A172_CENTRAL_NERVOUS_SYSTEM brain_cancer 67.5
#> A204_SOFT_TISSUE NA NA
#> A2058_SKIN melanoma NA
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM Brain Cancer NA
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST breast_cancer 88.7
#> ZR7530_BREAST breast_cancer NA
#> doublingTimeFromVendor ethnicity
#> <character> <character>
#> A101D_SKIN NA Caucasian
#> A1207_CENTRAL_NERVOUS_SYSTEM NA Caucasian
#> A172_CENTRAL_NERVOUS_SYSTEM NA Caucasian
#> A204_SOFT_TISSUE NA Caucasian
#> A2058_SKIN NA Caucasian
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA Asian
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST NA Caucasian
#> ZR7530_BREAST 110 hrs African_american
#> fractionGenomeAltered freezingMedium
#> <numeric> <character>
#> A101D_SKIN 0.7564 NA
#> A1207_CENTRAL_NERVOUS_SYSTEM 0.6374 NA
#> A172_CENTRAL_NERVOUS_SYSTEM 0.6671 5%DMSO
#> A204_SOFT_TISSUE 0.0248 NA
#> A2058_SKIN 0.2263 NA
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM 0.4721 NA
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST 0.3956 5%DMSO
#> ZR7530_BREAST 0.4669 NA
#> genomeDoublings geographicDistribution
#> <integer> <character>
#> A101D_SKIN 1 NA
#> A1207_CENTRAL_NERVOUS_SYSTEM 1 NA
#> A172_CENTRAL_NERVOUS_SYSTEM 0 NA
#> A204_SOFT_TISSUE 0 NA
#> A2058_SKIN 0 NA
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM 1 NA
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST 1 NA
#> ZR7530_BREAST 0 NA
#> growthMedium histSubtype1
#> <character> <character>
#> A101D_SKIN NA NS
#> A1207_CENTRAL_NERVOUS_SYSTEM NA NS
#> A172_CENTRAL_NERVOUS_SYSTEM DMEM +10%FBS astrocytoma_Grade_IV
#> A204_SOFT_TISSUE NA NS
#> A2058_SKIN NA NS
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA astrocytoma_Grade_IV
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST RPMI-1640 + 10% FBS ductal_carcinoma
#> ZR7530_BREAST NA ductal_carcinoma
#> histSubtype2 histSubtype3
#> <character> <character>
#> A101D_SKIN NS NS
#> A1207_CENTRAL_NERVOUS_SYSTEM NS NS
#> A172_CENTRAL_NERVOUS_SYSTEM glioblastoma_multifo.. NS
#> A204_SOFT_TISSUE NS NS
#> A2058_SKIN NS NS
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM glioblastoma_multifo.. NS
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST NS NS
#> ZR7530_BREAST NS NS
#> histology lifeStage
#> <character> <character>
#> A101D_SKIN Malignant_Melanoma NA
#> A1207_CENTRAL_NERVOUS_SYSTEM Glioma NA
#> A172_CENTRAL_NERVOUS_SYSTEM Glioma NA
#> A204_SOFT_TISSUE Rhabdoid_Tumour pediatric
#> A2058_SKIN Malignant_Melanoma NA
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM Glioma NA
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST Carcinoma NA
#> ZR7530_BREAST Carcinoma NA
#> mutationCount mutationRate name
#> <integer> <numeric> <character>
#> A101D_SKIN 253 78.1451 A101D
#> A1207_CENTRAL_NERVOUS_SYSTEM 93 NA A1207
#> A172_CENTRAL_NERVOUS_SYSTEM 268 135.6191 A172
#> A204_SOFT_TISSUE 205 92.6719 A-204
#> A2058_SKIN 556 164.6769 A2058
#> ... ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM 357 162.4756 YKG1
#> YMB1E_BREAST 261 NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE 542 NA NA
#> ZR751_BREAST 251 65.3901 ZR-75-1
#> ZR7530_BREAST 385 175.8765 ZR-75-30
#> oncotreeCode pathologistAnnotation
#> <character> <character>
#> A101D_SKIN SKCM Skin:Melanoma
#> A1207_CENTRAL_NERVOUS_SYSTEM GBM NA
#> A172_CENTRAL_NERVOUS_SYSTEM GBM CNS:Glioma_HighGrade
#> A204_SOFT_TISSUE ERMS Soft_Tissue:Sarcoma_..
#> A2058_SKIN SKCM Skin:Melanoma
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM GBM CNS:Glioma_HighGrade
#> YMB1E_BREAST CUP NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE CUP NA
#> ZR751_BREAST BRCA Breast:Carcinoma
#> ZR7530_BREAST BRCA Breast:Carcinoma
#> ploidy primarySite
#> <numeric> <character>
#> A101D_SKIN 2.63 Skin
#> A1207_CENTRAL_NERVOUS_SYSTEM 2.79 Central_Nervous_System
#> A172_CENTRAL_NERVOUS_SYSTEM 1.97 Central_Nervous_System
#> A204_SOFT_TISSUE 2.00 Soft_Tissue
#> A2058_SKIN 2.21 Skin
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM 3.19 Central_Nervous_System
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST 3.30 Breast
#> ZR7530_BREAST 1.98 Breast
#> proteomics10plexId proteomicsTmtLabel
#> <integer> <character>
#> A101D_SKIN 38 126
#> A1207_CENTRAL_NERVOUS_SYSTEM NA NA
#> A172_CENTRAL_NERVOUS_SYSTEM 24 127n
#> A204_SOFT_TISSUE 23 126
#> A2058_SKIN 3 129n
#> ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA NA
#> YMB1E_BREAST NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA
#> ZR751_BREAST 10 129c
#> ZR7530_BREAST NA NA
#> purity race sampleCount
#> <numeric> <character> <integer>
#> A101D_SKIN 1 Caucasian 1
#> A1207_CENTRAL_NERVOUS_SYSTEM 1 NA 1
#> A172_CENTRAL_NERVOUS_SYSTEM 1 NA 1
#> A204_SOFT_TISSUE 1 NA 1
#> A2058_SKIN 1 Caucasian 1
#> ... ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM 0.98 NA 1
#> YMB1E_BREAST NA NA 1
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA 1
#> ZR751_BREAST 1.00 Caucasian 1
#> ZR7530_BREAST 1.00 African_American 1
#> sampleType sex siteOfFinding
#> <character> <character> <character>
#> A101D_SKIN Primary Male NA
#> A1207_CENTRAL_NERVOUS_SYSTEM NA Female NA
#> A172_CENTRAL_NERVOUS_SYSTEM Primary Male NA
#> A204_SOFT_TISSUE Primary Female NA
#> A2058_SKIN Metastasis Male lymph_node
#> ... ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM Primary Female NA
#> YMB1E_BREAST NA NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA NA
#> ZR751_BREAST Metastasis Female ascites
#> ZR7530_BREAST Metastasis Female ascites
#> siteSubtype1 siteSubtype2 siteSubtype3
#> <character> <character> <character>
#> A101D_SKIN NS NS NS
#> A1207_CENTRAL_NERVOUS_SYSTEM NS NS NS
#> A172_CENTRAL_NERVOUS_SYSTEM brain NS NS
#> A204_SOFT_TISSUE striated_muscle NS NS
#> A2058_SKIN NS NS NS
#> ... ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM temporal_lobe NS NS
#> YMB1E_BREAST NA NA NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA NA NA
#> ZR751_BREAST NS NS NS
#> ZR7530_BREAST NS NS NS
#> supplements tmbNonsynonymous tumorType
#> <character> <numeric> <character>
#> A101D_SKIN NA 8.40000 melanoma
#> A1207_CENTRAL_NERVOUS_SYSTEM NA 3.20000 glioma
#> A172_CENTRAL_NERVOUS_SYSTEM NA 9.06667 glioma
#> A204_SOFT_TISSUE NA 7.00000 soft_tissue
#> A2058_SKIN NA 18.66667 melanoma
#> ... ... ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM NA 12.0667 glioma
#> YMB1E_BREAST NA 8.9000 NA
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA 18.2000 NA
#> ZR751_BREAST NA 8.5000 breast
#> ZR7530_BREAST NA 12.9667 breast
#> typeRefined
#> <character>
#> A101D_SKIN melanoma
#> A1207_CENTRAL_NERVOUS_SYSTEM glioma
#> A172_CENTRAL_NERVOUS_SYSTEM glioma
#> A204_SOFT_TISSUE soft_tissue
#> A2058_SKIN melanoma
#> ... ...
#> YKG1_CENTRAL_NERVOUS_SYSTEM glioma
#> YMB1E_BREAST breast
#> YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA
#> ZR751_BREAST breast
#> ZR7530_BREAST breast