cgdsr (version 1.3.0)

cgdsr-getMutationData: Get mutation data for cancer study

Description

Queries the CGDS API and returns mutation data for a given case set and list of genes.

Usage

# S3 method for CGDS
getMutationData(x, caseList, geneticProfile, genes, ...)

Arguments

x

A CGDS object (required)

caseList

A case list ID

geneticProfile

A genetic profile ID with mutation data

genes

A vector of query genes

...

Not used.

Value

A data.frame with rows for each sample/case, rownames corresponding to case IDs, and columns corresponding to:

1. entrez_gene_id: Entrez gene ID

2. gene_symbol: HUGO gene symbol

3. sequencing_center: Sequencer Center responsible for identifying this mutation.

4. mutation_status: somatic or germline mutation status. all mutations returned will be of type somatic.

5. age_at_diagnosis: Age at diagnosis.

6. mutation_type: mutation type, such as nonsense, missense, or frameshift_ins.

7. validation_status: validation status. Usually valid, invalid, or unknown.

8. amino_acid_change: amino acid change resulting from the mutation.

9. functional_impact_score: predicted functional impact score, as predicted by Mutation Assessor.

10. xvar_link: Link to the Mutation Assessor web site.

11. xvar_link_pdb: Link to the Protein Data Bank (PDB) View within Mutation Assessor web site.

12. xvar_link_msa: Link the Multiple Sequence Alignment (MSA) view within the Mutation Assessor web site.

13. chr: chromosome where mutation occurs.

14. start_position: start position of mutation.

15. end_position: end position of mutation

References

cBio Cancer Genomics Portal: http://www.cbioportal.org/

See Also

cgdsr,CGDS

Examples

# NOT RUN {
# Create CGDS object
mycgds = CGDS("http://www.cbioportal.org/")

getCancerStudies(mycgds)

# Get available case lists (collection of samples) for a given cancer study 
# Get Extended Mutation Data for EGFR and PTEN in TCGA GBM

# }
# NOT RUN {
getMutationData(mycgds,gbm_tcga_all,gbm_tcga_mutations,c('EGFR','PTEN'))
# }