getClinSites: getClinSites captures the clinical targetable sites of oncokb...

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

getClinSites captures the clinical targetable sites of oncokb based on the mutation status

Description

getClinSites captures the clinical targetable sites of oncokb based on the mutation status

Usage

getClinSites(maf, Patient_ID = NULL)

Arguments

maf	Maf or MafList object generated by readMaf function
Patient_ID	Patient_ID. See specific patient.

Details

We match the drivers genes between maf files and clinical sites in oncokb. We only match the gene names, whereas ignoring the cancer types and gene alterations. The main targertable alterations include gene fusions (like BCR-ABL1 fusion), Oncogenic mutations, Exon deletions/insertion, Amplifications, Deletions and Singles-nucleotide mutation (BRAC V600E). Please mannual check the mutation status.

Examples

library(MesKit)
data.type <- "split1"

maf <- readMaf(
  mafFile = system.file(package = "MPTevol", "extdata", sprintf("meskit.%s.mutation.txt", data.type)),
  ccfFile = system.file(package = "MPTevol", "extdata", sprintf("meskit.%s.CCF.txt", data.type)),
  clinicalFile = system.file(package = "MPTevol", "extdata", sprintf("meskit.%s.clinical.txt", data.type)),
  refBuild = "hg19",
  ccf.conf.level = 0.95
)

# see clinical targetable sites
sites <- getClinSites(maf)

# see one patinets
sites <- getClinSites(maf, Patient_ID = "Breast")

# View data
DT::datatable(sites)

qingjian1991/MPTevol documentation built on Jan. 30, 2023, 10:16 p.m.