Acute Myeloid Leukemia
LAML-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( LAML )
ExperimentList class object of length 11:
[1] LAML_CNASNP-20160128: RaggedExperiment with 874897 rows and 392 columns
[2] LAML_CNVSNP-20160128: RaggedExperiment with 28324 rows and 380 columns
[3] LAML_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[4] LAML_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 191 columns
[5] LAML_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[6] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns
[7] LAML_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 173 columns
[8] LAML_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 173 columns
[9] LAML_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 179 columns
[10] LAML_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 194 columns
[11] LAML_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 194 columns
> rownames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] character(0)
[["LAML_CNVSNP-20160128"]] character(0)
[["LAML_GISTIC_AllByGene-20160128"]] character(0)
[["LAML_GISTIC_Peaks-20160128"]] 1 5 6 7 8 9 2 10 11 12 13 14 15 3 16 4
[["LAML_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LAML_Mutation-20160128"]] character(0)
[["LAML_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeqGene-20160128"]] AADACL3 AADACL4 ABCA4 ... XGPY2 XKRY2 ZFY
[["LAML_Methylation_methyl27-20160128"]] cg00000292 cg00002426 ... cg27665659
...
<1 more element>
> colnames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] TCGA-AB-2802-03A-01D-0756-21 ...
[["LAML_CNVSNP-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_AllByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_Peaks-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_ThresholdedByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_Mutation-20160128"]] TCGA-AB-2802-03B-01W-0728-08 ...
[["LAML_RNASeq2Gene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeq2GeneNorm-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeqGene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_Methylation_methyl27-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 LAML_CNASNP-20160128 23.5 Mb
2 LAML_CNVSNP-20160128 0.9 Mb
3 LAML_GISTIC_AllByGene-20160128 39.5 Mb
4 LAML_GISTIC_Peaks-20160128 0.1 Mb
5 LAML_GISTIC_ThresholdedByGene-20160128 39.5 Mb
6 LAML_Mutation-20160128 2.8 Mb
7 LAML_RNASeq2Gene-20160128 29.6 Mb
8 LAML_RNASeq2GeneNorm-20160128 29.6 Mb
9 LAML_RNASeqGene-20160128 29.8 Mb
10 LAML_Methylation_methyl27-20160128 4.9 Mb
11 LAML_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)
80 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
120.000 120.000 0.748 0.586 0.918
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
18.00 44.75 57.00 55.02 67.00 88.00
vital_status:
0 1
67 133
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 91.5 273.0 355.7 489.0 1706.0 80
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 296.2 699.0 913.5 1506.8 2861.0 132
tumor_tissue_site:
bone marrow NA's
199 1
gender:
female male
91 109
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2001 2004 2006 2006 2008 2010
race:
asian black or african american white
2 15 181
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
3 194 3
Including an additional 478 columns