sv: An example IMPACT cBioPortal mutation data set in API format
In AxelitoMartin/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

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An example IMPACT cBioPortal mutation data set in API format

Description

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

Usage

sv

Format

A data frame with structural variants from Abida et al. JCO Precis Oncol 2017. Retrieved from cBioPortal.There are 94 observations and 29 variables.

A data frame with 94 rows and 44 variables:

uniqueSampleKey: character COLUMN_DESCRIPTION
uniquePatientKey: character COLUMN_DESCRIPTION
molecularProfileId: character COLUMN_DESCRIPTION
sampleId: MSKCC Sample ID
patientId: Patient ID
studyId: Indicator for Abida et al. 2017 study
site1EntrezGeneId: integer COLUMN_DESCRIPTION
site1HugoSymbol: Character w/ 31 levels, Column containing HUGO symbols genes for first site of fusion
site1EnsemblTranscriptId: character COLUMN_DESCRIPTION
site1Chromosome: character COLUMN_DESCRIPTION
site1Position: integer COLUMN_DESCRIPTION
site1Contig: character COLUMN_DESCRIPTION
site1Region: character COLUMN_DESCRIPTION
site1RegionNumber: integer COLUMN_DESCRIPTION
site1Description: character COLUMN_DESCRIPTION
site2EntrezGeneId: integer COLUMN_DESCRIPTION
site2HugoSymbol: Character w/ 21 levels, Column containing all HUGO symbols genes for second site of fusion
site2EnsemblTranscriptId: character COLUMN_DESCRIPTION
site2Chromosome: character COLUMN_DESCRIPTION
site2Position: integer COLUMN_DESCRIPTION
site2Contig: character COLUMN_DESCRIPTION
site2Region: character COLUMN_DESCRIPTION
site2RegionNumber: integer COLUMN_DESCRIPTION
site2Description: character COLUMN_DESCRIPTION
site2EffectOnFrame: character COLUMN_DESCRIPTION
ncbiBuild: character COLUMN_DESCRIPTION
dnaSupport: Factor, all are yes in this data
rnaSupport: Factor, all are unknown in this data
normalReadCount: integer COLUMN_DESCRIPTION
tumorReadCount: integer COLUMN_DESCRIPTION
normalVariantCount: integer COLUMN_DESCRIPTION
tumorVariantCount: integer COLUMN_DESCRIPTION
normalPairedEndReadCount: integer COLUMN_DESCRIPTION
tumorPairedEndReadCount: integer COLUMN_DESCRIPTION
normalSplitReadCount: integer COLUMN_DESCRIPTION
tumorSplitReadCount: integer COLUMN_DESCRIPTION
annotation: character COLUMN_DESCRIPTION
breakpointType: character COLUMN_DESCRIPTION
connectionType: character COLUMN_DESCRIPTION
eventInfo: character COLUMN_DESCRIPTION
variantClass: character COLUMN_DESCRIPTION
length: integer COLUMN_DESCRIPTION
comments: character COLUMN_DESCRIPTION
svStatus: character COLUMN_DESCRIPTION