LIHC-v2.1.0: Liver hepatocellular carcinoma

In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Liver hepatocellular carcinoma

Description

A document describing the TCGA cancer code

Details

> experiments( LIHC )
ExperimentList class object of length 12:
 [1] LIHC_CNASNP-20160128: RaggedExperiment with 363628 rows and 760 columns
 [2] LIHC_CNVSNP-20160128: RaggedExperiment with 93328 rows and 760 columns
 [3] LIHC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
 [4] LIHC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 59 rows and 370 columns
 [5] LIHC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
 [6] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
 [7] LIHC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 423 columns
 [8] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns
 [9] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns
 [10] LIHC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns
 [11] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17690 rows and 423 columns
 [12] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns

> rownames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] character(0)
[["LIHC_CNVSNP-20160128"]] character(0)
[["LIHC_GISTIC_AllByGene-20160128"]] character(0)
[["LIHC_GISTIC_Peaks-20160128"]] 28 29 1 2 3 30 4 31 ... 23 24 58 25 26 59 60
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LIHC_Mutation-20160128"]] character(0)
[["LIHC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>

> colnames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_CNVSNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_AllByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_Peaks-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ...
[["LIHC_RNASeq2Gene-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ...
[["LIHC_RNASeqGene-20160128"]] TCGA-BC-4073-01B-02R-A131-07 ...
[["LIHC_RPPAArray-20160128"]] TCGA-BC-4072-01B-21-A40L-20 ...
[["LIHC_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ...
...
<2 more elements>

Sizes of each ExperimentList element:

                                    assay size.Mb
1                    LIHC_CNASNP-20160128  9.9 Mb
2                    LIHC_CNVSNP-20160128  2.7 Mb
3          LIHC_GISTIC_AllByGene-20160128 73.5 Mb
4              LIHC_GISTIC_Peaks-20160128  0.3 Mb
5  LIHC_GISTIC_ThresholdedByGene-20160128 73.3 Mb
6                  LIHC_Mutation-20160128 16.8 Mb
7               LIHC_RNASeq2Gene-20160128 68.8 Mb
8                LIHC_RNASeqGene-20160128  6.6 Mb
9                 LIHC_RPPAArray-20160128  0.4 Mb
10             LIHC_miRNASeqGene-20160128  3.6 Mb
11          LIHC_RNASeq2GeneNorm-20160128 59.3 Mb
12              LIHC_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)

   245 observations deleted due to missingness 
       n events median 0.95LCL 0.95UCL
[1,] 132    132   1.14   0.956    1.63


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

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  16.00   51.00   61.00   59.27   69.00   87.00       4 

vital_status:
  0   1 
245 132 

days_to_death:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
    9.0   194.8   417.5   672.1   837.0  3258.0     245 

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
    0.0   395.8   649.5   885.8  1222.0  3675.0     133 

tumor_tissue_site:
liver 
  377 



pathology_N_stage:
  n0   n1   nx NA's 
 257    4  115    1 

pathology_M_stage:
 m0  m1  mx 
272   4 101 

gender:
female   male 
   122    255 

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   1995    2008    2011    2010    2012    2013       3 

radiation_therapy:
  no  yes NA's 
 345    9   23 

histological_type:
         fibrolamellar carcinoma         hepatocellular carcinoma 
                               3                              367 
hepatocholangiocarcinoma (mixed) 
                               7 

residual_tumor:
  r0   r1   r2   rx NA's 
 330   17    1   22    7 

race:
american indian or alaska native                            asian 
                               2                              161 
       black or african american                            white 
                              17                              187 
                            NA's 
                              10 

ethnicity:
    hispanic or latino not hispanic or latino                   NA's 
                    18                    340                     19 

Including an additional 1218 columns

waldronlab/curatedTCGAData documentation built on Feb. 7, 2024, 1:12 p.m.