Rectum adenocarcinoma
READ-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( READ )
ExperimentList class object of length 16:
[1] READ_CNASeq-20160128: RaggedExperiment with 56380 rows and 70 columns
[2] READ_CNASNP-20160128: RaggedExperiment with 156806 rows and 316 columns
[3] READ_CNVSNP-20160128: RaggedExperiment with 35765 rows and 316 columns
[4] READ_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[5] READ_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 55 rows and 165 columns
[6] READ_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[7] READ_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 76 columns
[8] READ_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[9] READ_Mutation-20160128: RaggedExperiment with 22075 rows and 69 columns
[10] READ_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 105 columns
[11] READ_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 72 columns
[12] READ_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 105 columns
[13] READ_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 72 columns
[14] READ_RPPAArray-20160128: SummarizedExperiment with 208 rows and 131 columns
[15] READ_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[16] READ_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 106 columns
> rownames( READ )
CharacterList of length 16
[["READ_CNASeq-20160128"]] character(0)
[["READ_CNASNP-20160128"]] character(0)
[["READ_CNVSNP-20160128"]] character(0)
[["READ_GISTIC_AllByGene-20160128"]] character(0)
[["READ_GISTIC_Peaks-20160128"]] 23 24 25 1 2 26 27 ... 54 55 18 19 20 56 57
[["READ_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["READ_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["READ_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["READ_Mutation-20160128"]] character(0)
[["READ_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<6 more elements>
> colnames( READ )
CharacterList of length 16
[["READ_CNASeq-20160128"]] TCGA-AF-2691-01A-01D-1167-02 ...
[["READ_CNASNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_CNVSNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_AllByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_Peaks-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_ThresholdedByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_miRNASeqGene-20160128"]] TCGA-AF-2687-01A-02T-1735-13 ...
[["READ_mRNAArray-20160128"]] TCGA-AF-2689-11A-01R-1758-07 ...
[["READ_Mutation-20160128"]] TCGA-AF-2689-01A-01W-0831-10 ... TCGA-AG-A036-01
[["READ_RNASeq2Gene-20160128"]] TCGA-AF-2687-01A-02R-1736-07 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 READ_CNASeq-20160128 1.5 Mb
2 READ_CNASNP-20160128 4.3 Mb
3 READ_CNVSNP-20160128 1.1 Mb
4 READ_GISTIC_AllByGene-20160128 34.7 Mb
5 READ_GISTIC_Peaks-20160128 0.2 Mb
6 READ_GISTIC_ThresholdedByGene-20160128 34.5 Mb
7 READ_miRNASeqGene-20160128 0.5 Mb
8 READ_mRNAArray-20160128 12 Mb
9 READ_Mutation-20160128 9.6 Mb
10 READ_RNASeq2Gene-20160128 19 Mb
11 READ_RNASeq2GeneNorm_illuminaga-20160128 13.8 Mb
12 READ_RNASeq2GeneNorm_illuminahiseq-20160128 19 Mb
13 READ_RNASeqGene-20160128 13.8 Mb
14 READ_RPPAArray-20160128 0.3 Mb
15 READ_Methylation_methyl27-20160128 4.9 Mb
16 READ_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)
142 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
27.00 27.00 2.00 1.44 3.25
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
31.00 57.00 66.00 64.37 72.00 90.00
vital_status:
0 1
141 28
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
59.0 347.5 730.0 786.1 1193.0 1741.0 142
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 366.0 625.0 779.5 1096.0 3932.0 28
tumor_tissue_site:
rectum NA's
166 3
pathology_M_stage:
m0 m1 m1a mx NA's
128 22 2 14 3
gender:
female male
77 92
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2007 2009 2008 2010 2012
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.0 292.2 863.0 1420.1 2214.5 3667.0 161
radiation_therapy:
no yes NA's
114 22 33
histological_type:
rectal adenocarcinoma rectal mucinous adenocarcinoma
150 13
NA's
6
tumor_stage:
stage iia NA's
1 168
residual_tumor:
r0 r1 r2 rx NA's
126 2 12 5 24
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.692 3.000 31.000 10
ethnicity:
hispanic or latino not hispanic or latino NA's
1 84 84
Including an additional 2242 columns