TCGAretriever-package: Retrieve Genomic and Clinical Data from CBioPortal

In dami82/TCGAretriever: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

Retrieve Genomic and Clinical Data from CBioPortal

Description

The Cancer Genome Atlas (TCGA) is a scientific and medical program aimed at improving our understanding of Cancer Biology. Part of the TCGA Datasets (free-access tier) are hosted on cBioPortal, which is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. TCGAretriever helps accessing and downloading TCGA data via the cBioPortal API. Features of TCGAretriever are:

• it is simple and reliable

• it is tailored for downloading large volumes of data

Author(s)

Damiano Fantini, [e-mail]

References

• https://www.data-pulse.com/dev_site/TCGAretriever/

• http://www.cbioportal.org/

• https://www.cancer.gov/ccg/research/genome-sequencing/tcga

See Also

Useful links:

• https://www.data-pulse.com/dev_site/TCGAretriever/

Examples

# List available Adenoid Cystic Carcinoma (acyc) Studies.
# Set `dryrun = FALSE` (default option) in production!
all_studies <- get_cancer_studies(dryrun = TRUE)
acyc_ids <- grep('acyc', all_studies$studyId, value = TRUE)
print(acyc_ids)


# List blca_tcga profiles.
# Set `dryrun = FALSE` (default option) in production!
get_genetic_profiles(csid = 'blca_tcga', dryrun = TRUE)


# List blca_tcga case lists.
# Set `dryrun = FALSE` (default option) in production!
get_case_lists(csid = 'blca_tcga', dryrun = TRUE)


# Retrieve expression data.
# Set `dryrun = FALSE` (default option) in production!
my_genes <- c('PTEN', 'TP53')
get_molecular_data(case_list_id = 'blca_tcga_3way_complete', 
                   gprofile_id = 'blca_tcga_rna_seq_v2_mrna', 
                   glist = my_genes, dryrun = TRUE)

dami82/TCGAretriever documentation built on Feb. 2, 2024, 12:06 p.m.