mutations: An example IMPACT cBioPortal mutation data set in API format
In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

mutations

R Documentation

An example IMPACT cBioPortal mutation data set in API format

This set contains a random sample of 200 patients from publicly available prostate cancer data from cBioPortal. The file is in API format.

mutations

A data frame with mutations from Abida et al. JCO Precis Oncol 2017. Retrieved from cBioPortal.There are 725 observations and 29 variables.

hugoGeneSymbol: Character w/ 324 levels, Column containing all HUGO symbols genes
entrezGeneId: Entrez Gene ID
sampleId: MSKCC Sample ID
patientId: Patient ID
studyId: Indicator for Abida et al. 2017 study
center: Cancer Center ID
mutationStatus: Somatic or germ-line mutation status
variantType: Mutation variant type
chr: Chromosome mutation observed on
endPosition: End Position
fisValue: fisValue
functionalImpactScore: functionalImpactScore
keyword: keyword
linkMsa: linkMsa
linkPdb: linkPdb
linkXvar: linkXvar
molecularProfileId: molecularProfileId
mutationType: mutationType
ncbiBuild: ncbiBuild
proteinChange: proteinChange
proteinPosEnd: proteinPosEnd
proteinPosStart: proteinPosStart
referenceAllele: referenceAllele
refseqMrnaId: refseqMrnaId
startPosition: startPosition
uniquePatientKey: uniquePatientKey
uniqueSampleKey: uniqueSampleKey
validationStatus: validationStatus
variantAllele: variantAllele