Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
DLBC-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( DLBC )
ExperimentList class object of length 11:
[1] DLBC_CNASNP-20160128: RaggedExperiment with 44725 rows and 94 columns
[2] DLBC_CNVSNP-20160128: RaggedExperiment with 9343 rows and 94 columns
[3] DLBC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[4] DLBC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 39 rows and 48 columns
[5] DLBC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[6] DLBC_Mutation-20160128: RaggedExperiment with 16918 rows and 48 columns
[7] DLBC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 48 columns
[8] DLBC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 33 columns
[9] DLBC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 47 columns
[10] DLBC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17665 rows and 48 columns
[11] DLBC_Methylation-20160128: SummarizedExperiment with 485577 rows and 48 columns
> rownames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] character(0)
[["DLBC_CNVSNP-20160128"]] character(0)
[["DLBC_GISTIC_AllByGene-20160128"]] character(0)
[["DLBC_GISTIC_Peaks-20160128"]] 15 17 16 1 2 18 19 ... 36 37 12 38 39 13 40
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["DLBC_Mutation-20160128"]] character(0)
[["DLBC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["DLBC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["DLBC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["DLBC_RNASeq2GeneNorm-20160128"]] A1BG A2LD1 A2ML1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_CNVSNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_AllByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_Peaks-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_Mutation-20160128"]] TCGA-FA-8693-01A-11D-2397-10 ...
[["DLBC_RNASeq2Gene-20160128"]] TCGA-FA-8693-01A-11R-2404-07 ...
[["DLBC_RPPAArray-20160128"]] TCGA-FA-8693-01A-21-A45K-20 ...
[["DLBC_miRNASeqGene-20160128"]] TCGA-FA-8693-01A-11R-2401-13 ...
[["DLBC_RNASeq2GeneNorm-20160128"]] TCGA-FA-8693-01 ... TCGA-VB-A8QN-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 DLBC_CNASNP-20160128 1.2 Mb
2 DLBC_CNVSNP-20160128 0.3 Mb
3 DLBC_GISTIC_AllByGene-20160128 12.5 Mb
4 DLBC_GISTIC_Peaks-20160128 0.1 Mb
5 DLBC_GISTIC_ThresholdedByGene-20160128 12.4 Mb
6 DLBC_Mutation-20160128 12.6 Mb
7 DLBC_RNASeq2Gene-20160128 10.1 Mb
8 DLBC_RPPAArray-20160128 0.1 Mb
9 DLBC_miRNASeqGene-20160128 0.5 Mb
10 DLBC_RNASeq2GeneNorm-20160128 8.7 Mb
11 DLBC_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)
39 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 9 9 1.63 0.858 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
23.00 46.00 57.50 56.27 67.00 82.00
vital_status:
0 1
39 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
58 313 595 1505 1252 6425 39
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 616 946 1328 1581 5980 9
gender:
female male
26 22
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1987 2009 2011 2009 2012 2013
radiation_therapy:
no yes NA's
40 7 1
histological_type:
diffuse large b-cell lymphoma (dlbcl) nos (any anatomic site nodal or extranodal)
41
primary dlbcl of the cns
3
primary mediastinal (thymic) dlbcl
4
race:
asian black or african american white
18 1 29
ethnicity:
hispanic or latino not hispanic or latino
12 36
Including an additional 607 columns