Lung adenocarcinoma
LUAD.RdA document describing the TCGA cancer code
Details
> experiments( LUAD )
ExperimentList class object of length 14:
[1] LUAD_CNASeq-20160128: RaggedExperiment with 399592 rows and 249 columns
[2] LUAD_CNASNP-20160128: RaggedExperiment with 501475 rows and 1095 columns
[3] LUAD_CNVSNP-20160128: RaggedExperiment with 115836 rows and 1095 columns
[4] LUAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[5] LUAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 73 rows and 516 columns
[6] LUAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[7] LUAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 498 columns
[8] LUAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 32 columns
[9] LUAD_Mutation-20160128: RaggedExperiment with 72541 rows and 230 columns
[10] LUAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 576 columns
[11] LUAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 162 columns
[12] LUAD_RPPAArray-20160128: SummarizedExperiment with 223 rows and 365 columns
[13] LUAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 89 columns
[14] LUAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 492 columns
> rownames( LUAD )
CharacterList of length 14
[["LUAD_CNASeq-20160128"]] character(0)
[["LUAD_CNASNP-20160128"]] character(0)
[["LUAD_CNVSNP-20160128"]] character(0)
[["LUAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LUAD_GISTIC_Peaks-20160128"]] chr1:1-32049393 ... chr22:46723702-51304566
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LUAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LUAD_Mutation-20160128"]] character(0)
[["LUAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( LUAD )
CharacterList of length 14
[["LUAD_CNASeq-20160128"]] TCGA-05-4249-01A-01D-1103-02 ...
[["LUAD_CNASNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_CNVSNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_AllByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_Peaks-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_miRNASeqGene-20160128"]] TCGA-05-4384-01A-01T-1754-13 ...
[["LUAD_mRNAArray-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
[["LUAD_Mutation-20160128"]] TCGA-05-4249-01A-01D-1105-08 ...
[["LUAD_RNASeq2GeneNorm-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUAD_CNASeq-20160128 10.8 Mb
2 LUAD_CNASNP-20160128 13.7 Mb
3 LUAD_CNVSNP-20160128 3.4 Mb
4 LUAD_GISTIC_AllByGene-20160128 4.9 Mb
5 LUAD_GISTIC_Peaks-20160128 0.1 Mb
6 LUAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LUAD_miRNASeqGene-20160128 0.1 Mb
8 LUAD_mRNAArray-20160128 1.1 Mb
9 LUAD_Mutation-20160128 92.9 Mb
10 LUAD_RNASeq2GeneNorm-20160128 1.3 Mb
11 LUAD_RNASeqGene-20160128 1.3 Mb
12 LUAD_RPPAArray-20160128 0.1 Mb
13 LUAD_Methylation_methyl27-20160128 4.9 Mb
14 LUAD_Methylation_methyl450-20160128 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)
336 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
184.00 184.00 1.70 1.37 2.00
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
33.00 59.00 66.00 65.22 72.00 88.00 31
vital_status:
0 1
332 188
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 297.8 619.0 791.4 1120.0 4961.0 336
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 459.5 670.0 968.7 1139.0 7248.0 193
tumor_tissue_site:
lung
520
gender:
female male
279 241
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1991 2007 2010 2008 2011 2013 19
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 96.5 141.0 327.6 386.0 1178.0 513
radiation_therapy:
no yes NA's
413 61 46
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 78.55 100.00 100.00 382
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.50 40.00 41.79 50.00 154.00 165
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1930 1956 1965 1965 1972 1999 241
residual_tumor:
r0 r1 r2 rx NA's
347 13 4 26 130
race:
american indian or alaska native asian
1 8
black or african american white
53 392
NA's
66
ethnicity:
hispanic or latino not hispanic or latino NA's
7 388 125
Including an additional 2607 columns