Adrenocortical carcinoma
ACC-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( ACC )
ExperimentList class object of length 11:
[1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 180 columns
[2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 180 columns
[3] ACC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[4] ACC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 42 rows and 90 columns
[5] ACC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[6] ACC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[7] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
[8] ACC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 79 columns
[9] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 79 columns
[10] ACC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 46 columns
[11] ACC_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] character(0)
[["ACC_CNVSNP-20160128"]] character(0)
[["ACC_GISTIC_AllByGene-20160128"]] character(0)
[["ACC_GISTIC_Peaks-20160128"]] 19 1 20 21 22 2 24 ... 41 42 14 15 16 43 44
[["ACC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ACC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ACC_Mutation-20160128"]] character(0)
[["ACC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_CNVSNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_AllByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_Peaks-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_ThresholdedByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_miRNASeqGene-20160128"]] TCGA-OR-A5J1-01A-11R-A29W-13 ...
[["ACC_Mutation-20160128"]] TCGA-OR-A5J1-01A-11D-A29I-10 ...
[["ACC_RNASeq2Gene-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RNASeq2GeneNorm-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RPPAArray-20160128"]] TCGA-OR-A5J2-01A-21-A39K-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 ACC_CNASNP-20160128 2.2 Mb
2 ACC_CNVSNP-20160128 0.6 Mb
3 ACC_GISTIC_AllByGene-20160128 20.5 Mb
4 ACC_GISTIC_Peaks-20160128 0.1 Mb
5 ACC_GISTIC_ThresholdedByGene-20160128 20.4 Mb
6 ACC_miRNASeqGene-20160128 0.8 Mb
7 ACC_Mutation-20160128 12.6 Mb
8 ACC_RNASeq2Gene-20160128 14.9 Mb
9 ACC_RNASeq2GeneNorm-20160128 14.9 Mb
10 ACC_RPPAArray-20160128 0.1 Mb
11 ACC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
58 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
34.00 34.00 1.51 1.34 3.03
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 35.50 48.50 47.16 60.00 83.00
vital_status:
0 1
58 34
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 399.0 551.5 854.6 1202.2 2405.0 58
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
383.0 917.8 1453.5 1781.6 2339.2 4673.0 34
tumor_tissue_site:
adrenal
92
pathologic_stage:
stage i stage ii stage iii stage iv NA's
9 44 19 18 2
pathology_T_stage:
t1 t2 t3 t4 NA's
9 49 11 21 2
pathology_N_stage:
n0 n1 NA's
80 10 2
gender:
female male
60 32
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1997 2005 2008 2007 2011 2012
radiation_therapy:
no yes NA's
71 18 3
histological_type:
adrenocortical carcinoma- myxoid type
1
adrenocortical carcinoma- oncocytic type
4
adrenocortical carcinoma- usual type
87
residual_tumor:
r0 r1 r2 rx NA's
64 7 12 6 3
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.548 0.500 52.000 61
race:
asian black or african american white
2 1 78
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
8 40 44
Including an additional 806 columns