Brain Lower Grade Glioma
LGG-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( LGG )
ExperimentList class object of length 13:
[1] LGG_CNASeq-20160128: RaggedExperiment with 6360 rows and 104 columns
[2] LGG_CNASNP-20160128: RaggedExperiment with 411918 rows and 1015 columns
[3] LGG_CNVSNP-20160128: RaggedExperiment with 79791 rows and 1015 columns
[4] LGG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[5] LGG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 46 rows and 513 columns
[6] LGG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[7] LGG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 526 columns
[8] LGG_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 27 columns
[9] LGG_Mutation-20160128: RaggedExperiment with 9885 rows and 286 columns
[10] LGG_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 530 columns
[11] LGG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 530 columns
[12] LGG_RPPAArray-20160128: SummarizedExperiment with 201 rows and 435 columns
[13] LGG_Methylation-20160128: SummarizedExperiment with 485577 rows and 530 columns
> rownames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] character(0)
[["LGG_CNASNP-20160128"]] character(0)
[["LGG_CNVSNP-20160128"]] character(0)
[["LGG_GISTIC_AllByGene-20160128"]] character(0)
[["LGG_GISTIC_Peaks-20160128"]] 21 22 1 2 23 3 24 25 ... 45 16 17 46 18 47 48
[["LGG_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LGG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LGG_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LGG_Mutation-20160128"]] character(0)
[["LGG_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] TCGA-CS-4938-01B-11D-1891-02 ...
[["LGG_CNASNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_CNVSNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_AllByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_Peaks-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_ThresholdedByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_miRNASeqGene-20160128"]] TCGA-CS-4938-01B-11R-1895-13 ...
[["LGG_mRNAArray-20160128"]] TCGA-CS-4942-01A-01R-1470-07 ...
[["LGG_Mutation-20160128"]] TCGA-CS-4938-01B-11D-1893-08 ...
[["LGG_RNASeq2Gene-20160128"]] TCGA-CS-4938-01B-11R-1896-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LGG_CNASeq-20160128 0.2 Mb
2 LGG_CNASNP-20160128 11.3 Mb
3 LGG_CNVSNP-20160128 2.4 Mb
4 LGG_GISTIC_AllByGene-20160128 100.5 Mb
5 LGG_GISTIC_Peaks-20160128 0.3 Mb
6 LGG_GISTIC_ThresholdedByGene-20160128 100.4 Mb
7 LGG_miRNASeqGene-20160128 4.4 Mb
8 LGG_mRNAArray-20160128 5.9 Mb
9 LGG_Mutation-20160128 4.2 Mb
10 LGG_RNASeq2Gene-20160128 85.5 Mb
11 LGG_RNASeq2GeneNorm-20160128 85.5 Mb
12 LGG_RPPAArray-20160128 0.8 Mb
13 LGG_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)
391 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
125.00 125.00 2.23 1.87 2.83
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.00 32.00 41.00 42.93 53.00 86.00 2
vital_status:
0 1 NA's
389 126 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7 438 814 1219 1547 5166 391
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-1.0 384.0 629.0 880.1 1147.0 6423.0 127
tumor_tissue_site:
central nervous system NA's
515 1
gender:
female male NA's
230 285 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2008 2011 2009 2012 2013 1
radiation_therapy:
no yes NA's
186 296 34
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 80.00 90.00 86.64 100.00 100.00 209
histological_type:
astrocytoma oligoastrocytoma oligodendroglioma NA's
194 130 191 1
race:
american indian or alaska native asian
1 8
black or african american white
21 475
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
32 449 35
Including an additional 1764 columns