all-data: Somatic Cancer Alterations Data Sets

In juliangehring/SomaticCancerAlterations: Somatic Cancer Alterations

Description

Data sets with studies of somatic cancer alterations.

Details

Currently, the data sets include somatic mutations (SNVs and indels) of the publically available TCGA studies. Further studies will be included in the future.

For details on the TCGA mutation calls, please see the TCGA documentation https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer. Please note that the mutational calling was performed by different centers. The original '*.maf' files can be obtained from the TCGA data portal https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/.

After importing, the data is automatically processed to improve consistency across studies and remove common artifacts in the annotation. The most obvious changes are:

• Only studies cleared for unrestricted usage are included (see http://cancergenome.nih.gov/publications/publicationguidelines).

• Only studies processed by the Broad Instutite are considered at the moment.

• All variants located on the mitochondrium are mapped to the sequence identifier 'MT' (note that the original files contain both 'MT' and 'M' mixed).

• All locations are now consistent with the 1000genomes reference sequence (NCBI37 coordinates).

About the TCGA data:

“All data generated by The Cancer Genome Atlas (TCGA) Research Network are made open to the public through the Data Coordinating Center and the TCGA Data Portal.” For details on the usage of the data, please have a look at http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines.

Value

A 'GRanges' object for each study. Each row corresponds to a somatic variant reported in the respective study, with the coordinates refering to the location on the reference genome.

References

https://tcga-data.nci.nih.gov/tcga/

See Also

SomaticCancerAlterations-functions

SomaticCancerAlterations-package

Examples

all_datasets = scaListDatasets()
grl = scaLoadDatasets(all_datasets[1])

juliangehring/SomaticCancerAlterations documentation built on Jan. 1, 2021, 7:12 a.m.