CESC-v2.1.0: Cervical squamous cell carcinoma and endocervical...
In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
CESC-v2.1.0 R Documentation
Cervical squamous cell carcinoma and endocervical adenocarcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( CESC )
ExperimentList class object of length 12:
[1] CESC_CNASeq-20160128: RaggedExperiment with 7834 rows and 100 columns
[2] CESC_CNASNP-20160128: RaggedExperiment with 267855 rows and 586 columns
[3] CESC_CNVSNP-20160128: RaggedExperiment with 59450 rows and 586 columns
[4] CESC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[5] CESC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 60 rows and 295 columns
[6] CESC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[7] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
[8] CESC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 309 columns
[9] CESC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 173 columns
[10] CESC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 312 columns
[11] CESC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18162 rows and 309 columns
[12] CESC_Methylation-20160128: SummarizedExperiment with 485577 rows and 312 columns
> rownames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] character(0)
[["CESC_CNASNP-20160128"]] character(0)
[["CESC_CNVSNP-20160128"]] character(0)
[["CESC_GISTIC_AllByGene-20160128"]] character(0)
[["CESC_GISTIC_Peaks-20160128"]] 27 1 28 2 3 29 4 30 ... 23 58 59 24 60 25 61
[["CESC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CESC_Mutation-20160128"]] character(0)
[["CESC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CESC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CESC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] TCGA-C5-A1BQ-01C-11D-A20X-26 ...
[["CESC_CNASNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_CNVSNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_AllByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_Peaks-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_Mutation-20160128"]] TCGA-BI-A0VR-01A-11D-A10S-08 ...
[["CESC_RNASeq2Gene-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
[["CESC_RPPAArray-20160128"]] TCGA-2W-A8YY-01A-21-A40H-20 ...
[["CESC_miRNASeqGene-20160128"]] TCGA-2W-A8YY-01A-11R-A37P-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 CESC_CNASeq-20160128 0.3 Mb
2 CESC_CNASNP-20160128 7.3 Mb
3 CESC_CNVSNP-20160128 1.8 Mb
4 CESC_GISTIC_AllByGene-20160128 59.3 Mb
5 CESC_GISTIC_Peaks-20160128 0.3 Mb
6 CESC_GISTIC_ThresholdedByGene-20160128 59.1 Mb
7 CESC_Mutation-20160128 32.9 Mb
8 CESC_RNASeq2Gene-20160128 50.9 Mb
9 CESC_RPPAArray-20160128 0.3 Mb
10 CESC_miRNASeqGene-20160128 2.7 Mb
11 CESC_RNASeq2GeneNorm-20160128 45.1 Mb
12 CESC_Methylation-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)
235 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 72 72 1.7 1.39 2.29
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 38.0 46.0 48.2 56.0 88.0 2
vital_status:
0 1
235 72
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 349.5 620.0 881.3 1069.5 4086.0 235
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 374 688 1071 1362 6408 72
tumor_tissue_site:
cervical
307
pathology_N_stage:
n0 n1 nx NA's
135 60 67 45
pathology_M_stage:
m0 m1 mx NA's
116 10 131 50
gender:
female
307
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
radiation_therapy:
no yes NA's
55 129 123
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
ethnicity:
hispanic or latino not hispanic or latino NA's
24 171 112
weight_kg_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.25 70.50 73.04 83.75 210.00 29
tumor_status:
tumor free with tumor NA's
201 80 26
tobacco_smoking_year_stopped:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1995 2003 2000 2010 2013 264
tobacco_smoking_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
tobacco_smoking_history:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 1.000 1.829 2.000 5.000 44
agebegansmokinginyears:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.00 16.00 18.00 21.14 24.00 44.00 222
radiation_therapy_status:
completed as planned treatment not completed NA's
29 3 275
pregnancies_count_total:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 2.00 3.00 3.61 5.00 15.00 40
pregnancies_count_stillbirth:
0 1 3 NA's
106 5 1 195
pregnancy_spontaneous_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.5442 1.0000 6.0000 160
pregnancies_count_live_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.250 2.000 2.844 4.000 11.000 45
pregnancy_therapeutic_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.8525 1.0000 13.0000 185
pregnancies_count_ectopic:
0 1 2 NA's
104 11 1 191
lymph_node_location:
lymph_node_location_positive_pathology_name|lymph_node_location_positive_pathology_text
307
menopause_status:
indeterminate (neither pre or postmenopausal)
3
peri (6-12 months since last menstrual period)
25
post (prior bilateral ovariectomy or >12 mo since lmp with no prior hysterectomy)
84
pre (<6 months since lmp and no prior bilateral ovariectomy and not on estrogen replacement)
125
NA's
70
lymphovascular_involvement:
absent present NA's
72 80 155
lymph_nodes_examined_he_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
lymph_nodes_examined:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.00 13.00 21.00 22.28 29.00 63.00 127
keratinization_squamous_cell:
keratinizing squamous cell carcinoma
55
non-keratinizing squamous cell carcinoma
120
NA's
132
initial_pathologic_dx_year:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
hysterectomy_type:
hysterectomy_performed_type|hysterectomy_performed_text
307
history_hormonal_contraceptives_use:
current user former user never used NA's
15 54 90 148
height_cm_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
132 157 160 161 165 183 43
corpus_involvement:
absent present NA's
99 19 189
chemo_concurrent_type:
carboplatin cisplatin other NA's
7 104 2 194
cervix_suv_results:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 8.70 12.00 13.22 16.92 28.80 290
cause_of_death:
cardiopulmonary arrest lung cancer renal failure
1 1 1
NA's
304
age_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
20.00 38.00 46.00 48.27 56.50 88.00
Including an additional 1330 columns
waldronlab/curatedTCGAData documentation built on Nov. 4, 2024, 7:57 a.m.
R Package Documentation
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| CESC-v2.1.0 | R Documentation |
Cervical squamous cell carcinoma and endocervical adenocarcinoma
Description
A document describing the TCGA cancer code
Details
> experiments( CESC )
ExperimentList class object of length 12:
[1] CESC_CNASeq-20160128: RaggedExperiment with 7834 rows and 100 columns
[2] CESC_CNASNP-20160128: RaggedExperiment with 267855 rows and 586 columns
[3] CESC_CNVSNP-20160128: RaggedExperiment with 59450 rows and 586 columns
[4] CESC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[5] CESC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 60 rows and 295 columns
[6] CESC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[7] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
[8] CESC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 309 columns
[9] CESC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 173 columns
[10] CESC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 312 columns
[11] CESC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18162 rows and 309 columns
[12] CESC_Methylation-20160128: SummarizedExperiment with 485577 rows and 312 columns
> rownames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] character(0)
[["CESC_CNASNP-20160128"]] character(0)
[["CESC_CNVSNP-20160128"]] character(0)
[["CESC_GISTIC_AllByGene-20160128"]] character(0)
[["CESC_GISTIC_Peaks-20160128"]] 27 1 28 2 3 29 4 30 ... 23 58 59 24 60 25 61
[["CESC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CESC_Mutation-20160128"]] character(0)
[["CESC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CESC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CESC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] TCGA-C5-A1BQ-01C-11D-A20X-26 ...
[["CESC_CNASNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_CNVSNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_AllByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_Peaks-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_Mutation-20160128"]] TCGA-BI-A0VR-01A-11D-A10S-08 ...
[["CESC_RNASeq2Gene-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
[["CESC_RPPAArray-20160128"]] TCGA-2W-A8YY-01A-21-A40H-20 ...
[["CESC_miRNASeqGene-20160128"]] TCGA-2W-A8YY-01A-11R-A37P-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 CESC_CNASeq-20160128 0.3 Mb
2 CESC_CNASNP-20160128 7.3 Mb
3 CESC_CNVSNP-20160128 1.8 Mb
4 CESC_GISTIC_AllByGene-20160128 59.3 Mb
5 CESC_GISTIC_Peaks-20160128 0.3 Mb
6 CESC_GISTIC_ThresholdedByGene-20160128 59.1 Mb
7 CESC_Mutation-20160128 32.9 Mb
8 CESC_RNASeq2Gene-20160128 50.9 Mb
9 CESC_RPPAArray-20160128 0.3 Mb
10 CESC_miRNASeqGene-20160128 2.7 Mb
11 CESC_RNASeq2GeneNorm-20160128 45.1 Mb
12 CESC_Methylation-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)
235 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 72 72 1.7 1.39 2.29
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 38.0 46.0 48.2 56.0 88.0 2
vital_status:
0 1
235 72
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 349.5 620.0 881.3 1069.5 4086.0 235
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 374 688 1071 1362 6408 72
tumor_tissue_site:
cervical
307
pathology_N_stage:
n0 n1 nx NA's
135 60 67 45
pathology_M_stage:
m0 m1 mx NA's
116 10 131 50
gender:
female
307
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
radiation_therapy:
no yes NA's
55 129 123
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
ethnicity:
hispanic or latino not hispanic or latino NA's
24 171 112
weight_kg_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.25 70.50 73.04 83.75 210.00 29
tumor_status:
tumor free with tumor NA's
201 80 26
tobacco_smoking_year_stopped:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1995 2003 2000 2010 2013 264
tobacco_smoking_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
tobacco_smoking_history:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 1.000 1.829 2.000 5.000 44
agebegansmokinginyears:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.00 16.00 18.00 21.14 24.00 44.00 222
radiation_therapy_status:
completed as planned treatment not completed NA's
29 3 275
pregnancies_count_total:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 2.00 3.00 3.61 5.00 15.00 40
pregnancies_count_stillbirth:
0 1 3 NA's
106 5 1 195
pregnancy_spontaneous_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.5442 1.0000 6.0000 160
pregnancies_count_live_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.250 2.000 2.844 4.000 11.000 45
pregnancy_therapeutic_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.8525 1.0000 13.0000 185
pregnancies_count_ectopic:
0 1 2 NA's
104 11 1 191
lymph_node_location:
lymph_node_location_positive_pathology_name|lymph_node_location_positive_pathology_text
307
menopause_status:
indeterminate (neither pre or postmenopausal)
3
peri (6-12 months since last menstrual period)
25
post (prior bilateral ovariectomy or >12 mo since lmp with no prior hysterectomy)
84
pre (<6 months since lmp and no prior bilateral ovariectomy and not on estrogen replacement)
125
NA's
70
lymphovascular_involvement:
absent present NA's
72 80 155
lymph_nodes_examined_he_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
lymph_nodes_examined:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.00 13.00 21.00 22.28 29.00 63.00 127
keratinization_squamous_cell:
keratinizing squamous cell carcinoma
55
non-keratinizing squamous cell carcinoma
120
NA's
132
initial_pathologic_dx_year:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
hysterectomy_type:
hysterectomy_performed_type|hysterectomy_performed_text
307
history_hormonal_contraceptives_use:
current user former user never used NA's
15 54 90 148
height_cm_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
132 157 160 161 165 183 43
corpus_involvement:
absent present NA's
99 19 189
chemo_concurrent_type:
carboplatin cisplatin other NA's
7 104 2 194
cervix_suv_results:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 8.70 12.00 13.22 16.92 28.80 290
cause_of_death:
cardiopulmonary arrest lung cancer renal failure
1 1 1
NA's
304
age_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
20.00 38.00 46.00 48.27 56.50 88.00
Including an additional 1330 columns
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