Cholangiocarcinoma
CHOL-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( CHOL )
ExperimentList class object of length 11:
[1] CHOL_CNASNP-20160128: RaggedExperiment with 39698 rows and 85 columns
[2] CHOL_CNVSNP-20160128: RaggedExperiment with 7570 rows and 85 columns
[3] CHOL_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[4] CHOL_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 19 rows and 36 columns
[5] CHOL_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[6] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns
[7] CHOL_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 45 columns
[8] CHOL_RPPAArray-20160128: SummarizedExperiment with 192 rows and 30 columns
[9] CHOL_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 45 columns
[10] CHOL_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18002 rows and 45 columns
[11] CHOL_Methylation-20160128: SummarizedExperiment with 485577 rows and 45 columns
> rownames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] character(0)
[["CHOL_CNVSNP-20160128"]] character(0)
[["CHOL_GISTIC_AllByGene-20160128"]] character(0)
[["CHOL_GISTIC_Peaks-20160128"]] 4 1 5 6 7 8 9 10 ... 13 3 14 15 18 16 17 20
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CHOL_Mutation-20160128"]] character(0)
[["CHOL_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CHOL_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CHOL_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CHOL_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<1 more element>
> colnames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_CNVSNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_AllByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_Peaks-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_Mutation-20160128"]] TCGA-3X-AAV9-01A-72D-A417-09 ...
[["CHOL_RNASeq2Gene-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ...
[["CHOL_RPPAArray-20160128"]] TCGA-3X-AAV9-01A-81-A45N-20 ...
[["CHOL_miRNASeqGene-20160128"]] TCGA-3X-AAV9-01A-72R-A41D-13 ...
[["CHOL_RNASeq2GeneNorm-20160128"]] TCGA-3X-AAV9-01 ... TCGA-ZU-A8S4-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 CHOL_CNASNP-20160128 1.1 Mb
2 CHOL_CNVSNP-20160128 0.2 Mb
3 CHOL_GISTIC_AllByGene-20160128 10.2 Mb
4 CHOL_GISTIC_Peaks-20160128 0 Mb
5 CHOL_GISTIC_ThresholdedByGene-20160128 10.1 Mb
6 CHOL_Mutation-20160128 4.6 Mb
7 CHOL_RNASeq2Gene-20160128 9.6 Mb
8 CHOL_RPPAArray-20160128 0.1 Mb
9 CHOL_miRNASeqGene-20160128 0.5 Mb
10 CHOL_RNASeq2GeneNorm-20160128 8.4 Mb
11 CHOL_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)
18 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 18 18 1.37 0.742 2.53
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 56.50 66.50 63.03 72.00 82.00
vital_status:
0 1
18 18
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
21.0 195.2 500.0 592.9 731.0 1939.0 18
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.0 539.8 942.5 936.6 1394.0 1976.0 18
tumor_tissue_site:
bile duct
36
pathology_T_stage:
t1 t2 t2a t2b t3
19 6 2 4 5
pathology_N_stage:
n0 n1 nx
26 5 5
pathology_M_stage:
m0 m1 mx
28 5 3
gender:
female male
20 16
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2005 2010 2011 2010 2012 2013
radiation_therapy:
no NA's
35 1
histological_type:
cholangiocarcinoma; distal cholangiocarcinoma; hilar/perihilar
2 4
cholangiocarcinoma; intrahepatic
30
residual_tumor:
r0 r1 rx
28 5 3
race:
asian black or african american white
3 2 31
ethnicity:
hispanic or latino not hispanic or latino NA's
2 33 1
Including an additional 622 columns