HNSC: Head and Neck squamous cell carcinoma
In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
HNSC R Documentation
Head and Neck squamous cell carcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( HNSC )
ExperimentList class object of length 12:
[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_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
[8] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
[9] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 566 columns
[10] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
[11] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
[12] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns
> rownames( HNSC )
CharacterList of length 12
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["HNSC_GISTIC_Peaks-20160128"]] chr1:1-27864255 ... chr21:41298805-43485528
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["HNSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( HNSC )
CharacterList of length 12
[["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_miRNASeqGene-20160128"]] TCGA-4P-AA8J-01A-11R-A39B-13 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2GeneNorm-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeqGene-20160128"]] TCGA-BA-4074-01A-01R-1436-07 ...
...
<2 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 4.9 Mb
5 HNSC_GISTIC_Peaks-20160128 0.1 Mb
6 HNSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 HNSC_miRNASeqGene-20160128 0.1 Mb
8 HNSC_Mutation-20160128 68.9 Mb
9 HNSC_RNASeq2GeneNorm-20160128 1.3 Mb
10 HNSC_RNASeqGene-20160128 1.3 Mb
11 HNSC_RPPAArray-20160128 0 Mb
12 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
223.00 223.00 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
See Also
HNSC-v2.0.1
waldronlab/curatedTCGAData documentation built on Nov. 4, 2024, 7:57 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| HNSC | R Documentation |
Head and Neck squamous cell carcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( HNSC )
ExperimentList class object of length 12:
[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_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
[8] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
[9] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 566 columns
[10] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
[11] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
[12] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns
> rownames( HNSC )
CharacterList of length 12
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["HNSC_GISTIC_Peaks-20160128"]] chr1:1-27864255 ... chr21:41298805-43485528
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["HNSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( HNSC )
CharacterList of length 12
[["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_miRNASeqGene-20160128"]] TCGA-4P-AA8J-01A-11R-A39B-13 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2GeneNorm-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeqGene-20160128"]] TCGA-BA-4074-01A-01R-1436-07 ...
...
<2 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 4.9 Mb
5 HNSC_GISTIC_Peaks-20160128 0.1 Mb
6 HNSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 HNSC_miRNASeqGene-20160128 0.1 Mb
8 HNSC_Mutation-20160128 68.9 Mb
9 HNSC_RNASeq2GeneNorm-20160128 1.3 Mb
10 HNSC_RNASeqGene-20160128 1.3 Mb
11 HNSC_RPPAArray-20160128 0 Mb
12 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
223.00 223.00 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
See Also
HNSC-v2.0.1
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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