LUSC: Lung squamous cell carcinoma
In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
LUSC R Documentation
Lung squamous cell carcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( LUSC )
ExperimentList class object of length 16:
[1] LUSC_CNACGH-20160128: RaggedExperiment with 87417 rows and 407 columns
[2] LUSC_CNASNP-20160128: RaggedExperiment with 543091 rows and 1035 columns
[3] LUSC_CNVSNP-20160128: RaggedExperiment with 134864 rows and 1032 columns
[4] LUSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[5] LUSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 78 rows and 501 columns
[6] LUSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[7] LUSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 387 columns
[8] LUSC_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 112 columns
[9] LUSC_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 154 columns
[10] LUSC_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 133 columns
[11] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
[12] LUSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 552 columns
[13] LUSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 240 columns
[14] LUSC_RPPAArray-20160128: SummarizedExperiment with 223 rows and 328 columns
[15] LUSC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 160 columns
[16] LUSC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 412 columns
> rownames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] character(0)
[["LUSC_CNASNP-20160128"]] character(0)
[["LUSC_CNVSNP-20160128"]] character(0)
[["LUSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LUSC_GISTIC_Peaks-20160128"]] chr1:1-31262836 ... chr22:45736500-51304566
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LUSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUSC_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["LUSC_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] AACS FSTL1 ELMO2 ... CTSC AQP7
...
<6 more elements>
> colnames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] TCGA-18-3406-01A-01D-1519-02 ...
[["LUSC_CNASNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_CNVSNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_AllByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_Peaks-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_miRNASeqGene-20160128"]] TCGA-18-5592-01A-01T-1634-13 ...
[["LUSC_mRNAArray_huex-20160128"]] TCGA-18-3406-01A-01R-1030-03 ...
[["LUSC_mRNAArray_TX_g4502a-20160128"]] TCGA-18-3406-01A-01R-0980-07 ...
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] TCGA-18-3406-01A-01R-1031-01 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUSC_CNACGH-20160128 2.5 Mb
2 LUSC_CNASNP-20160128 14.8 Mb
3 LUSC_CNVSNP-20160128 3.9 Mb
4 LUSC_GISTIC_AllByGene-20160128 4.9 Mb
5 LUSC_GISTIC_Peaks-20160128 0.1 Mb
6 LUSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LUSC_miRNASeqGene-20160128 0.1 Mb
8 LUSC_mRNAArray_huex-20160128 1.2 Mb
9 LUSC_mRNAArray_TX_g4502a-20160128 1.1 Mb
10 LUSC_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb
11 LUSC_Mutation-20160128 81 Mb
12 LUSC_RNASeq2GeneNorm-20160128 1.3 Mb
13 LUSC_RNASeqGene-20160128 1.3 Mb
14 LUSC_RPPAArray-20160128 0 Mb
15 LUSC_Methylation_methyl27-20160128 4.9 Mb
16 LUSC_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)
289 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
215.00 215.00 1.51 1.25 1.88
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
39.00 62.00 68.00 67.26 73.00 90.00 10
vital_status:
0 1
284 220
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.0 280.0 550.0 872.3 1110.5 5287.0 289
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 394 757 1049 1374 4765 221
tumor_tissue_site:
lung
504
pathology_N_stage:
n0 n1 n2 n3 nx
320 133 40 5 6
gender:
female male
131 373
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2005 2009 2008 2011 2013 25
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 298.8 706.0 904.8 1051.8 3724.0 436
radiation_therapy:
no yes NA's
387 53 64
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 0.0 80.0 60.3 90.0 100.0 338
histological_type:
lung basaloid squamous cell carcinoma
15
lung papillary squamous cell caricnoma
6
lung small cell squamous cell carcinoma
1
lung squamous cell carcinoma- not otherwise specified (nos)
482
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 31.12 50.00 52.91 64.50 240.00 77
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1933 1952 1960 1960 1968 1997 183
residual_tumor:
r0 r1 r2 rx NA's
401 12 4 23 64
race:
asian black or african american white
9 31 351
NA's
113
ethnicity:
hispanic or latino not hispanic or latino NA's
8 319 177
Including an additional 2238 columns
See Also
LUSC-v2.0.1
waldronlab/curatedTCGAData documentation built on Feb. 7, 2024, 1:12 p.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.
| LUSC | R Documentation |
Lung squamous cell carcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( LUSC )
ExperimentList class object of length 16:
[1] LUSC_CNACGH-20160128: RaggedExperiment with 87417 rows and 407 columns
[2] LUSC_CNASNP-20160128: RaggedExperiment with 543091 rows and 1035 columns
[3] LUSC_CNVSNP-20160128: RaggedExperiment with 134864 rows and 1032 columns
[4] LUSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[5] LUSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 78 rows and 501 columns
[6] LUSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[7] LUSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 387 columns
[8] LUSC_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 112 columns
[9] LUSC_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 154 columns
[10] LUSC_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 133 columns
[11] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
[12] LUSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 552 columns
[13] LUSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 240 columns
[14] LUSC_RPPAArray-20160128: SummarizedExperiment with 223 rows and 328 columns
[15] LUSC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 160 columns
[16] LUSC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 412 columns
> rownames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] character(0)
[["LUSC_CNASNP-20160128"]] character(0)
[["LUSC_CNVSNP-20160128"]] character(0)
[["LUSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LUSC_GISTIC_Peaks-20160128"]] chr1:1-31262836 ... chr22:45736500-51304566
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LUSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUSC_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["LUSC_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] AACS FSTL1 ELMO2 ... CTSC AQP7
...
<6 more elements>
> colnames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] TCGA-18-3406-01A-01D-1519-02 ...
[["LUSC_CNASNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_CNVSNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_AllByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_Peaks-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_miRNASeqGene-20160128"]] TCGA-18-5592-01A-01T-1634-13 ...
[["LUSC_mRNAArray_huex-20160128"]] TCGA-18-3406-01A-01R-1030-03 ...
[["LUSC_mRNAArray_TX_g4502a-20160128"]] TCGA-18-3406-01A-01R-0980-07 ...
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] TCGA-18-3406-01A-01R-1031-01 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUSC_CNACGH-20160128 2.5 Mb
2 LUSC_CNASNP-20160128 14.8 Mb
3 LUSC_CNVSNP-20160128 3.9 Mb
4 LUSC_GISTIC_AllByGene-20160128 4.9 Mb
5 LUSC_GISTIC_Peaks-20160128 0.1 Mb
6 LUSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LUSC_miRNASeqGene-20160128 0.1 Mb
8 LUSC_mRNAArray_huex-20160128 1.2 Mb
9 LUSC_mRNAArray_TX_g4502a-20160128 1.1 Mb
10 LUSC_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb
11 LUSC_Mutation-20160128 81 Mb
12 LUSC_RNASeq2GeneNorm-20160128 1.3 Mb
13 LUSC_RNASeqGene-20160128 1.3 Mb
14 LUSC_RPPAArray-20160128 0 Mb
15 LUSC_Methylation_methyl27-20160128 4.9 Mb
16 LUSC_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)
289 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
215.00 215.00 1.51 1.25 1.88
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
39.00 62.00 68.00 67.26 73.00 90.00 10
vital_status:
0 1
284 220
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.0 280.0 550.0 872.3 1110.5 5287.0 289
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 394 757 1049 1374 4765 221
tumor_tissue_site:
lung
504
pathology_N_stage:
n0 n1 n2 n3 nx
320 133 40 5 6
gender:
female male
131 373
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2005 2009 2008 2011 2013 25
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 298.8 706.0 904.8 1051.8 3724.0 436
radiation_therapy:
no yes NA's
387 53 64
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 0.0 80.0 60.3 90.0 100.0 338
histological_type:
lung basaloid squamous cell carcinoma
15
lung papillary squamous cell caricnoma
6
lung small cell squamous cell carcinoma
1
lung squamous cell carcinoma- not otherwise specified (nos)
482
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 31.12 50.00 52.91 64.50 240.00 77
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1933 1952 1960 1960 1968 1997 183
residual_tumor:
r0 r1 r2 rx NA's
401 12 4 23 64
race:
asian black or african american white
9 31 351
NA's
113
ethnicity:
hispanic or latino not hispanic or latino NA's
8 319 177
Including an additional 2238 columns
See Also
LUSC-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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