tcga: TCGA data

In UCLouvain-CBIO/rWSBIM1207: Companion Package for WSBIM1207 Course

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.

sampleID

a factor

patient

a character vector

type

a character vector

A1BG

a numeric vector

A1CF

a numeric vector

A2BP1

a numeric vector

A2LD1

a numeric vector

A2ML1

a numeric vector

clinical1: clinical data for 516 observations on the following 15 variables.

patientID

a character vector

tumor_tissue_site

a character vector

gender

a character vector

age_at_diagnosis

a numeric vector

vital_status

a numeric vector

days_to_death

a numeric vector

days_to_last_followup

a numeric vector

pathologic_stage

a character vector

pathology_T_stage

a character vector

pathology_N_stage

a character vector

pathology_M_stage

a character vector

smoking_history

a character vector

number_pack_years_smoked

a numeric vector

year_of_tobacco_smoking_onset

a numeric vector

stopped_smoking_year

a numeric vector

clinical2: small clinical data with 516 observations on the following 3 variables.

patientID

a character vector

gender

a character vector

years_at_diagnosis

a numeric vector

A clinical summary data with 2 observations on the following 3 variables.

gender

a 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 March 20, 2024, 4:20 a.m.