Glioblastoma multiforme
GBM-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( GBM )
ExperimentList class object of length 18:
[1] GBM_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 81512 rows and 438 columns
[2] GBM_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 57975 rows and 338 columns
[3] GBM_CNASNP-20160128: RaggedExperiment with 602338 rows and 1104 columns
[4] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
[5] GBM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[6] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
[7] GBM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[8] GBM_miRNAArray-20160128: SummarizedExperiment with 534 rows and 565 columns
[9] GBM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 0 columns
[10] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns
[11] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 502 columns
[12] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns
[13] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns
[14] GBM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 166 columns
[15] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns
[16] GBM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 244 columns
[17] GBM_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 285 columns
[18] GBM_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 154 columns
> rownames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["GBM_CNASNP-20160128"]] character(0)
[["GBM_CNVSNP-20160128"]] character(0)
[["GBM_GISTIC_AllByGene-20160128"]] character(0)
[["GBM_GISTIC_Peaks-20160128"]] 25 26 1 27 28 2 29 3 ... 65 22 23 66 67 24 68
[["GBM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["GBM_miRNAArray-20160128"]] ebv-miR-BART1-3p ... kshv-miR-K12-9*
[["GBM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["GBM_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
...
<8 more elements>
> colnames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] TCGA-02-0001-01C-01D-0185-02 ...
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-02-2466-01A-01D-0787-02 ...
[["GBM_CNASNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_CNVSNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_AllByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_Peaks-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_ThresholdedByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_miRNAArray-20160128"]] TCGA-02-0001-01C-01T-0179-07 ...
[["GBM_miRNASeqGene-20160128"]] character(0)
[["GBM_mRNAArray_huex-20160128"]] TCGA-02-0001-01C-01R-0178-03 ...
...
<8 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 GBM_CNACGH_CGH_hg_244a-20160128 2.3 Mb
2 GBM_CNACGH_CGH_hg_415k_g4124a-20160128 1.7 Mb
3 GBM_CNASNP-20160128 16.4 Mb
4 GBM_CNVSNP-20160128 4.2 Mb
5 GBM_GISTIC_AllByGene-20160128 112.7 Mb
6 GBM_GISTIC_Peaks-20160128 0.5 Mb
7 GBM_GISTIC_ThresholdedByGene-20160128 112.5 Mb
8 GBM_miRNAArray-20160128 2.5 Mb
9 GBM_miRNASeqGene-20160128 0.2 Mb
10 GBM_mRNAArray_huex-20160128 63.7 Mb
11 GBM_mRNAArray_TX_g4502a-20160128 70.5 Mb
12 GBM_mRNAArray_TX_ht_hg_u133a-20160128 50.1 Mb
13 GBM_Mutation-20160128 31 Mb
14 GBM_RNASeq2Gene-20160128 28.5 Mb
15 GBM_RNASeq2GeneNorm-20160128 28.5 Mb
16 GBM_RPPAArray-20160128 0.5 Mb
17 GBM_Methylation_methyl27-20160128 4.9 Mb
18 GBM_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
109 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
490.000 490.000 1.047 0.981 1.156
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.00 50.00 59.00 57.82 68.00 89.00 4
vital_status:
0 1 NA's
104 491 4
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 170.5 382.0 504.5 609.2 3881.0 109
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 156.2 261.0 479.4 628.0 2818.0 497
tumor_tissue_site:
brain NA's
595 4
gender:
female male NA's
230 365 4
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1989 2002 2006 2005 2009 2013 4
radiation_therapy:
no yes NA's
78 489 32
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 70.00 80.00 77.04 80.00 100.00 157
histological_type:
glioblastoma multiforme (gbm) treated primary gbm
31 20
untreated primary (de novo) gbm NA's
544 4
race:
asian black or african american white
13 51 506
NA's
29
ethnicity:
hispanic or latino not hispanic or latino NA's
13 489 97
Including an additional 4368 columns