HNSC-v2.1.0: Head and Neck squamous cell carcinoma

In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Head and Neck squamous cell carcinoma

Description

A document describing the TCGA cancer code

Details

> experiments( HNSC )
ExperimentList class object of length 13:
 [1] HNSC_CNASeq-20160128: RaggedExperiment with 32905 rows and 225 columns
 [2] HNSC_CNASNP-20160128: RaggedExperiment with 499142 rows and 1090 columns
 [3] HNSC_CNVSNP-20160128: RaggedExperiment with 110289 rows and 1089 columns
 [4] HNSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
 [5] HNSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 72 rows and 522 columns
 [6] HNSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
 [7] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
 [8] HNSC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 566 columns
 [9] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
 [10] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
 [11] HNSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
 [12] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18361 rows and 566 columns
 [13] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns

> rownames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] character(0)
[["HNSC_GISTIC_Peaks-20160128"]] 29 30 31 1 32 33 2 ... 25 26 70 71 72 27 73
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RPPAArray-20160128"]] 14-3-3_epsilon 4E-BP1 ... p90RSK_pT359_S363
...
<3 more elements>

> colnames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] TCGA-BA-4074-01A-01D-1431-02 ...
[["HNSC_CNASNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_CNVSNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_AllByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_Peaks-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2Gene-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeqGene-20160128"]] TCGA-BA-4074-01A-01R-1436-07 ...
[["HNSC_RPPAArray-20160128"]] TCGA-BA-4074-01A-21-2072-20 ...
...
<3 more elements>

Sizes of each ExperimentList element:

                                    assay  size.Mb
1                    HNSC_CNASeq-20160128     1 Mb
2                    HNSC_CNASNP-20160128  13.6 Mb
3                    HNSC_CNVSNP-20160128   3.3 Mb
4          HNSC_GISTIC_AllByGene-20160128 102.3 Mb
5              HNSC_GISTIC_Peaks-20160128   0.5 Mb
6  HNSC_GISTIC_ThresholdedByGene-20160128 102.1 Mb
7                  HNSC_Mutation-20160128  68.9 Mb
8               HNSC_RNASeq2Gene-20160128  91.2 Mb
9                HNSC_RNASeqGene-20160128  48.6 Mb
10                HNSC_RPPAArray-20160128   0.3 Mb
11             HNSC_miRNASeqGene-20160128   4.5 Mb
12          HNSC_RNASeq2GeneNorm-20160128  81.6 Mb
13              HNSC_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)

   305 observations deleted due to missingness 
       n events median 0.95LCL 0.95UCL
[1,] 223    223   1.18    1.06    1.35


---------------------------
Available sample meta-data:
---------------------------

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  19.00   53.00   61.00   60.91   69.00   89.00       1 

vital_status:
  0   1 
304 224 

days_to_death:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
    2.0   260.0   430.0   740.0   814.5  6417.0     305 

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   11.0   529.5   851.0  1042.9  1404.0  5480.0     225 

tumor_tissue_site:
head and neck 
          528 




pathology_M_stage:
  m0   m1   mx NA's 
 191    1   65  271 

gender:
female   male 
   142    386 

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   1992    2007    2010    2008    2011    2013       1 

days_to_last_known_alive:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   98.0   483.0   848.5  1226.9  1647.5  3930.0     506 

radiation_therapy:
  no  yes NA's 
 163  303   62 

histological_type:
                      head & neck squamous cell carcinoma 
                                                      517 
        head & neck squamous cell carcinoma basaloid type 
                                                       10 
head & neck squamous cell carcinoma, spindle cell variant 
                                                        1 

number_pack_years_smoked:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.      NA's 
  0.01685  25.00000  40.00000  45.75496  60.00000 300.00000       230 

year_of_tobacco_smoking_onset:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   1936    1959    1968    1967    1975    2001     246 

number_of_lymph_nodes:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  0.000   0.000   1.000   2.186   3.000  44.000     115 

race:
american indian or alaska native                            asian 
                               2                               11 
       black or african american                            white 
                              48                              452 
                            NA's 
                              15 

ethnicity:
    hispanic or latino not hispanic or latino                   NA's 
                    26                    465                     37 

Including an additional 1426 columns

waldronlab/curatedTCGAData documentation built on Nov. 4, 2024, 7:57 a.m.