Using RTCGA package to estimate a frequency of MDM2 duplications based on CNV data

Przemyslaw Biecek


RTCGA.cnv package

You need RTCGA.cnv package to use CNV scores.



To get scores for all cancers for selected gene or region one should use the get.region.cnv.score() function.

For example, MDM2 is located on chromosome 12 positions 69240000-69200000.

get.region.cnv.score <- function(chr="12", start=69240000, stop=69200000) {
  list_cnv <- data(package="RTCGA.cnv")
  datasets <- list_cnv$results[,"Item"]
  filtered <- lapply(datasets, function(dataname) {
    tmp <- get(dataname)
    tmp <- tmp[tmp$Chromosome == chr,]
    tmp <- tmp[pmin(tmp$Start, tmp$End) <= pmax(stop, start) & pmax(tmp$Start, tmp$End) >= pmin(stop, start),]
    data.frame(tmp, cohort=dataname)
  }), filtered)
MDM2.scores <- get.region.cnv.score(chr="12", start=69240000, stop=69200000)

# only one per patient
MDM2.scores$Sample <- substr(MDM2.scores$Sample, 1, 12)
MDM2.scores <- MDM2.scores[!duplicated(MDM2.scores$Sample),]

Let’s see where there are more than 3 copies of MDM2

cutoff <- log(3)/log(2)-1
MDM2cuted <- cut(MDM2.scores$Segment_Mean, c(0, cutoff, Inf), labels = c("<= 3", "> 3"))

And now we can calculate number of cases with <= or >3 copies od MDM2 in each cancer type.

table(MDM2.scores$cohort, MDM2cuted)