g3viz (version 1.1.5)

getMutationsFromCbioportal: Query cancer genomic mutation data from cBioPortal

Description

Retrieve and parse mutation data from cBioPortal by the given cBioPortal cancer study ID and the gene symbol.

Usage

getMutationsFromCbioportal(
  study.id,
  gene.symbol,
  output.file = NA,
  mutation.type.to.class.df = NA
)

Value

a data frame with columns

Hugo_Symbol

Hugo gene symbol

Protein_Change

Protein change information (cBioportal uses HGVSp format)

Sample_ID

Sample ID

Mutation_Type

mutation type, aka, variant classification.

Chromosome

chromosome

Start_Position

start position

End_Position

end position

Reference_Allele

reference allele

Variant_Allele

variant allele

Mutation_Class

mutation class (e.g., Truncating/Missense/Inframe/Other)

AA_Position

amino-acid position of the variant; if the variant is not in protein-coding region, NA

Arguments

study.id

cbioprotal study ID

gene.symbol

HGNC gene symbol.

output.file

if specified, output to a file in CSV format. Default is NA.

mutation.type.to.class.df

mapping table from mutation type to class. See mapMutationTypeToMutationClass for details. Default NA, which indicates to use default mappings.

Examples

if (FALSE) {
# Usage:
# cBioPortalData has officially replaced the defunct cgdsr.
# Search online for cgdsrMigration.html if interested.
library(cBioPortalData)
cbio <- cBioPortal()

# list all studies of cBioPortal
all.studies <- getStudies(cbio, buildReport = FALSE)

# First, select a cancer study that contains mutation data set ("caner_study_id")
# then, query genomic mutation data using a HGNC gene symbol,
# for example
mutation.dat <- getMutationsFromCbioportal("msk_impact_2017", "TP53")
mutation.dat <- getMutationsFromCbioportal("all_stjude_2016", "TP53")
}