Esophageal carcinoma

A document describing the TCGA cancer code

Details

> experiments( ESCA )
ExperimentList class object of length 13:
 [1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns
 [2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns
 [3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns
 [4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
 [5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns
 [6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
 [7] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns
 [8] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
 [9] ESCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 196 columns
 [10] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 196 columns
 [11] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns
 [12] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns
 [13] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns

> rownames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] character(0)
[["ESCA_CNASNP-20160128"]] character(0)
[["ESCA_CNVSNP-20160128"]] character(0)
[["ESCA_GISTIC_AllByGene-20160128"]] character(0)
[["ESCA_GISTIC_Peaks-20160128"]] 31 1 32 2 3 33 4 34 ... 73 74 29 75 76 77 78
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ESCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ESCA_Mutation-20160128"]] character(0)
[["ESCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ESCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>

> colnames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ...
[["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_miRNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37J-13 ...
[["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ...
[["ESCA_RNASeq2Gene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RNASeq2GeneNorm-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
...
<3 more elements>

Sizes of each ExperimentList element:

                                    assay size.Mb
1                    ESCA_CNASeq-20160128  0.5 Mb
2                    ESCA_CNASNP-20160128  5.5 Mb
3                    ESCA_CNVSNP-20160128  1.7 Mb
4          ESCA_GISTIC_AllByGene-20160128 38.3 Mb
5              ESCA_GISTIC_Peaks-20160128  0.2 Mb
6  ESCA_GISTIC_ThresholdedByGene-20160128 38.1 Mb
7              ESCA_miRNASeqGene-20160128  1.8 Mb
8                  ESCA_Mutation-20160128   45 Mb
9               ESCA_RNASeq2Gene-20160128 33.2 Mb
10          ESCA_RNASeq2GeneNorm-20160128 33.2 Mb
11               ESCA_RNASeqGene-20160128 42.8 Mb
12                ESCA_RPPAArray-20160128  0.2 Mb
13              ESCA_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)

   108 observations deleted due to missingness
      n  events  median 0.95LCL 0.95UCL
 77.000  77.000   0.962   0.677   1.353


---------------------------
Available sample meta-data:
---------------------------

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
  27.00   54.00   61.00   62.46   72.00   90.00

vital_status:
  0   1
108  77

days_to_death:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
    9.0   180.0   351.0   495.2   650.0  2532.0     108

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
    4.0   336.5   402.5   570.1   696.8  3714.0      77

tumor_tissue_site:
esophagus
      185




pathology_M_stage:
  m0   m1  m1a   mx NA's
 136    4    5   18   22

gender:
female   male
    27    158

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
   1998    2007    2011    2009    2012    2013       7

radiation_therapy:
  no  yes NA's
 124   43   18

karnofsky_performance_score:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
  20.00   60.00   80.00   73.82   90.00  100.00     117

histological_type:
    esophagus adenocarcinoma, nos esophagus squamous cell carcinoma
                               89                                96

number_pack_years_smoked:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
   1.00   17.62   30.00   34.48   47.25  102.00      87

residual_tumor:
  r0   r1   r2   rx NA's
 137   13    2    7   26

number_of_lymph_nodes:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
  0.000   0.000   1.000   2.526   4.000  21.000      50

race:
                    asian black or african american                     white
                       46                         5                       114
                     NA's
                       20

ethnicity:
    hispanic or latino not hispanic or latino                   NA's
                     6                     88                     91

Including an additional 940 columns