Thyroid carcinoma
THCA-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( THCA )
ExperimentList class object of length 13:
[1] THCA_CNASeq-20160128: RaggedExperiment with 5953 rows and 203 columns
[2] THCA_CNASNP-20160128: RaggedExperiment with 389998 rows and 1013 columns
[3] THCA_CNVSNP-20160128: RaggedExperiment with 55117 rows and 1013 columns
[4] THCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[5] THCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 38 rows and 499 columns
[6] THCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[7] THCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 569 columns
[8] THCA_Mutation-20160128: RaggedExperiment with 7458 rows and 405 columns
[9] THCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 568 columns
[10] THCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 568 columns
[11] THCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 4 columns
[12] THCA_RPPAArray-20160128: SummarizedExperiment with 175 rows and 224 columns
[13] THCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 567 columns
> rownames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] character(0)
[["THCA_CNASNP-20160128"]] character(0)
[["THCA_CNVSNP-20160128"]] character(0)
[["THCA_GISTIC_AllByGene-20160128"]] character(0)
[["THCA_GISTIC_Peaks-20160128"]] 1 10 11 12 2 13 3 14 ... 36 37 38 39 7 40 41
[["THCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THCA_Mutation-20160128"]] character(0)
[["THCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] TCGA-BJ-A0Z2-01A-11D-A10R-02 ...
[["THCA_CNASNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_CNVSNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_AllByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_Peaks-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_miRNASeqGene-20160128"]] TCGA-4C-A93U-01A-11R-A39B-13 ...
[["THCA_Mutation-20160128"]] TCGA-BJ-A0YZ-01A-11D-A10S-08 ...
[["THCA_RNASeq2Gene-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
[["THCA_RNASeq2GeneNorm-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 THCA_CNASeq-20160128 0.2 Mb
2 THCA_CNASNP-20160128 10.7 Mb
3 THCA_CNVSNP-20160128 1.8 Mb
4 THCA_GISTIC_AllByGene-20160128 97.8 Mb
5 THCA_GISTIC_Peaks-20160128 0.3 Mb
6 THCA_GISTIC_ThresholdedByGene-20160128 97.7 Mb
7 THCA_miRNASeqGene-20160128 4.8 Mb
8 THCA_Mutation-20160128 14 Mb
9 THCA_RNASeq2Gene-20160128 91.5 Mb
10 THCA_RNASeq2GeneNorm-20160128 91.5 Mb
11 THCA_RNASeqGene-20160128 3.2 Mb
12 THCA_RPPAArray-20160128 0.4 Mb
13 THCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
487 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
16.00 16.00 2.80 2.23 4.80
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
15.00 35.00 46.00 47.26 58.00 89.00
vital_status:
0 1
487 16
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
174 743 1021 1176 1631 2973 487
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 535 943 1220 1513 5423 16
tumor_tissue_site:
thyroid
503
pathology_N_stage:
n0 n1 n1a n1b nx
227 58 93 75 50
pathology_M_stage:
m0 m1 mx NA's
280 9 213 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1993 2008 2010 2009 2011 2013
radiation_therapy:
no yes NA's
181 306 16
radiation_exposure:
no yes NA's
423 17 63
extrathyroidal_extension:
minimal (t3) moderate/advanced (t4a) none
133 18 333
very advanced (t4b) NA's
1 18
residual_tumor:
r0 r1 r2 rx NA's
385 52 4 30 32
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 3.658 5.000 41.000 114
multifocality:
multifocal unifocal NA's
227 266 10
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.300 1.700 2.600 2.975 4.000 8.200 100
Including an additional 1481 columns