Liver hepatocellular carcinoma
LIHC.RdA document describing the TCGA cancer code
Details
> experiments( LIHC )
ExperimentList class object of length 11:
[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_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns
[7] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
[8] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 423 columns
[9] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns
[10] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns
[11] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns
> rownames( LIHC )
CharacterList of length 11
[["LIHC_CNASNP-20160128"]] character(0)
[["LIHC_CNVSNP-20160128"]] character(0)
[["LIHC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LIHC_GISTIC_Peaks-20160128"]] chr1:1-6847369 ... chr22:44205320-51304566
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LIHC_Mutation-20160128"]] character(0)
[["LIHC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( LIHC )
CharacterList of length 11
[["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_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ...
[["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ...
[["LIHC_RNASeq2GeneNorm-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 ...
...
<1 more element>
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 4.9 Mb
4 LIHC_GISTIC_Peaks-20160128 0.1 Mb
5 LIHC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 LIHC_miRNASeqGene-20160128 0.1 Mb
7 LIHC_Mutation-20160128 16.8 Mb
8 LIHC_RNASeq2GeneNorm-20160128 1.3 Mb
9 LIHC_RNASeqGene-20160128 1.3 Mb
10 LIHC_RPPAArray-20160128 0 Mb
11 LIHC_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)
245 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
132.000 132.000 1.144 0.956 1.633
---------------------------
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