tcgaViz (version 1.0.2)

tcga: Biological data

Description

A list of biological data: RNASeq data, phenotypic metadata and cell abundance.

Usage

data(tcga)

Details

• genes: RNASeq from The Cancer Genome Atlas (TCGA) database.

• phenotypes: Metadata from the TCGA database containing sample ID, sample type ID, sample type and primary disease.

• cells: Abundance estimates of cell types

Examples

data(tcga)
(df <- convert2biodata(
    algorithm = "Cibersort_ABS",
    disease = "breast invasive carcinoma",
    tissue = "Primary Tumor",
    gene_x = "ICOS"
))
(stats <- calculate_pvalue(df))
# \donttest{
plot(df, stats = stats)
# }