Pancreatic adenocarcinoma
PAAD.RdA document describing the TCGA cancer code
Details
> experiments( PAAD )
ExperimentList class object of length 10:
[1] PAAD_CNASNP-20160128: RaggedExperiment with 203871 rows and 368 columns
[2] PAAD_CNVSNP-20160128: RaggedExperiment with 34808 rows and 365 columns
[3] PAAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[4] PAAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 52 rows and 184 columns
[5] PAAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[6] PAAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 183 columns
[7] PAAD_Mutation-20160128: RaggedExperiment with 30357 rows and 150 columns
[8] PAAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 183 columns
[9] PAAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 123 columns
[10] PAAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 195 columns
> rownames( PAAD )
CharacterList of length 10
[["PAAD_CNASNP-20160128"]] character(0)
[["PAAD_CNVSNP-20160128"]] character(0)
[["PAAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["PAAD_GISTIC_Peaks-20160128"]] chr1:26795113-27650365 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["PAAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PAAD_Mutation-20160128"]] character(0)
[["PAAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PAAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PAAD_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( PAAD )
CharacterList of length 10
[["PAAD_CNASNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_CNVSNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_AllByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_Peaks-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_miRNASeqGene-20160128"]] TCGA-2J-AAB1-01A-11R-A41G-13 ...
[["PAAD_Mutation-20160128"]] TCGA-2J-AAB1-01A-11D-A40W-08 ...
[["PAAD_RNASeq2GeneNorm-20160128"]] TCGA-2J-AAB1-01A-11R-A41B-07 ...
[["PAAD_RPPAArray-20160128"]] TCGA-2J-AAB4-01A-21-A43K-20 ...
[["PAAD_Methylation-20160128"]] TCGA-2J-AAB1-01A-11D-A40Y-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 PAAD_CNASNP-20160128 5.6 Mb
2 PAAD_CNVSNP-20160128 1 Mb
3 PAAD_GISTIC_AllByGene-20160128 4.9 Mb
4 PAAD_GISTIC_Peaks-20160128 0.1 Mb
5 PAAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 PAAD_miRNASeqGene-20160128 0.1 Mb
7 PAAD_Mutation-20160128 111 Mb
8 PAAD_RNASeq2GeneNorm-20160128 1.3 Mb
9 PAAD_RPPAArray-20160128 0 Mb
10 PAAD_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)
85 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
100.000 100.000 1.079 0.967 1.315
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
35.00 57.00 65.00 64.86 73.00 88.00
vital_status:
0 1
85 100
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
12.0 228.5 394.0 459.5 596.5 2182.0 85
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 338.0 517.0 692.4 951.0 2741.0 100
tumor_tissue_site:
pancreas
185
pathology_N_stage:
n0 n1 n1b nx NA's
50 126 4 4 1
pathology_M_stage:
m0 m1 mx
85 5 95
gender:
female male
83 102
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2001 2010 2012 2011 2012 2013 1
radiation_therapy:
no yes NA's
125 45 15
histological_type:
pancreas-adenocarcinoma ductal type
154
pancreas-adenocarcinoma-other subtype
25
pancreas-colloid (mucinous non-cystic) carcinoma
4
pancreas-undifferentiated carcinoma
1
NA's
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.30 15.00 25.00 26.84 40.00 75.00 128
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1948 1960 1971 1971 1982 1993 138
residual_tumor:
r0 r1 r2 rx NA's
111 53 5 4 12
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 2.000 2.989 4.000 16.000 4
race:
asian black or african american white
11 7 162
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
5 137 43
Including an additional 960 columns