tcga {tcgaViz}

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

Note

Subset of thirty samples of invasive breast carcinoma data from primary tumor tissue. The cell type data are from a subset generated by the Cibersort_ABS algorithm (https://cibersortx.stanford.edu). For the complete dataset, please use:

path <- system.file("extdata", package = "tcgaViz")
load(file.path(path, "tcga.rda"))

Source

• dataset: gene expression RNAseq - Batch effects normalized mRNA data

• hub: https://pancanatlas.xenahubs.net

• cohort: TCGA Pan-Cancer (PANCAN)

• dataset ID: EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena

• download: https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/EB%2B%2BAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz (full metadata)

• samples: 11060

• version: 2016-12-29

• type of data: gene expression RNAseq

• unit: log2(norm_value+1)

• raw data: https://www.synapse.org/#!Synapse:syn4976369.3

• input data format: ROWs (identifiers) x COLUMNs (samples) (i.e. genomicMatrix)

Examples

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

plot(df, stats = stats)