tcga: TCGA data
In UCLouvain-CBIO/rWSBIM1207: Companion Package for WSBIM1207 Course
tcga R Documentation
TCGA data
Description
The Cancer Genome Atlas (TCGA) is a collaboration between the National
Cancer Institute (NCI) and the National Human Genome Research Institute
(NHGRI) that has generated multi-omics analyses (genomic, transcriptomic,
proteomic and epigenetic) in 33 types of cancer.
RNAseq and clinical data analysed here come from LUAD (lung adenocarcinoma)
tumors and corresponding patients.
TCGA clinical and RNAseq expression data extracted from the
curatedTCGAData package. See inst/scripts/tcga.R for
details.
Usage
data("expression")
data("clinical1")
data("clinical2")
data("clinical_table_ex1")
Format
expression: RNA expression data frame with 570 observations on
the following 8 variables.
sampleIDa factor
patienta character vector
typea character vector
A1BGa numeric vector
A1CFa numeric vector
A2BP1a numeric vector
A2LD1a numeric vector
A2ML1a numeric vector
clinical1: clinical data for 516 observations on the following
15 variables.
patientIDa character vector
tumor_tissue_sitea character vector
gendera character vector
age_at_diagnosisa numeric vector
vital_statusa numeric vector
days_to_deatha numeric vector
days_to_last_followupa numeric vector
pathologic_stagea character vector
pathology_T_stagea character vector
pathology_N_stagea character vector
pathology_M_stagea character vector
smoking_historya character vector
number_pack_years_smokeda numeric vector
year_of_tobacco_smoking_onseta numeric vector
stopped_smoking_yeara numeric vector
clinical2: small clinical data with 516 observations on the
following 3 variables.
patientIDa character vector
gendera character vector
years_at_diagnosisa numeric vector
A clinical summary data with 2 observations on the following 3
variables.
gendera character vector
- ‘current smoker’
a numeric vector
- ‘lifelong non-smoker’
a numeric vector
In addition, the clinical1.csv and expression.csv
function return the paths to these respective comma-separated value
spreadsheets. The expressions.csv function returns the path to
the expression data split by gene.
Examples
data(expression)
data(clinical1)
data(clinical2)
data(clinical_table_ex1)
UCLouvain-CBIO/rWSBIM1207 documentation built on June 18, 2024, 11:26 p.m.
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| tcga | R Documentation |
TCGA data
Description
The Cancer Genome Atlas (TCGA) is a collaboration between the National
Cancer Institute (NCI) and the National Human Genome Research Institute
(NHGRI) that has generated multi-omics analyses (genomic, transcriptomic,
proteomic and epigenetic) in 33 types of cancer.
RNAseq and clinical data analysed here come from LUAD (lung adenocarcinoma)
tumors and corresponding patients.
TCGA clinical and RNAseq expression data extracted from the
curatedTCGAData package. See inst/scripts/tcga.R for
details.
Usage
data("expression")
data("clinical1")
data("clinical2")
data("clinical_table_ex1")
Format
expression: RNA expression data frame with 570 observations on
the following 8 variables.
sampleIDa factor
patienta character vector
typea character vector
A1BGa numeric vector
A1CFa numeric vector
A2BP1a numeric vector
A2LD1a numeric vector
A2ML1a numeric vector
clinical1: clinical data for 516 observations on the following
15 variables.
patientIDa character vector
tumor_tissue_sitea character vector
gendera character vector
age_at_diagnosisa numeric vector
vital_statusa numeric vector
days_to_deatha numeric vector
days_to_last_followupa numeric vector
pathologic_stagea character vector
pathology_T_stagea character vector
pathology_N_stagea character vector
pathology_M_stagea character vector
smoking_historya character vector
number_pack_years_smokeda numeric vector
year_of_tobacco_smoking_onseta numeric vector
stopped_smoking_yeara numeric vector
clinical2: small clinical data with 516 observations on the
following 3 variables.
patientIDa character vector
gendera character vector
years_at_diagnosisa numeric vector
A clinical summary data with 2 observations on the following 3 variables.
gendera character vector
- ‘current smoker’
a numeric vector
- ‘lifelong non-smoker’
a numeric vector
In addition, the clinical1.csv and expression.csv
function return the paths to these respective comma-separated value
spreadsheets. The expressions.csv function returns the path to
the expression data split by gene.
Examples
data(expression)
data(clinical1)
data(clinical2)
data(clinical_table_ex1)
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