How to find TCGA samples with multiple chromosomal gains?

Question

[melissachua90]

I want to perform mutation analysis on TCGA data. How do I find samples that meet the following criteria: "multiple chromosomal gains (of at least one complete copy of the chromosome), including nearly universal gain of chromosomes 7 and 17 and less frequent gain of chromosomes 2, 3, 12, 16, and 20 "

library(maftools)
library(TCGAbiolinks)

query.kirp.snv <- GDCquery(
  project = "TCGA-KIRP", 
  data.category = "Simple Nucleotide Variation", 
  access = "open", 
  legacy = FALSE, 
  data.type = "Masked Somatic Mutation", 
  workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)
GDCdownload(query.kirp.snv)
maf.kirp <- GDCprepare(query.kirp.snv)
maf.kirp <- maf.kirp %>% read.maf

df <- datatable(getSampleSummary(maf.kirp), rownames = FALSE)