CNA_GDC

Check GISTIC results

library(plyr)
library(dplyr)
library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-COAD",
                  data.category = "Copy Number Variation",
                  data.type = "Gene Level Copy Number Scores",              
                  access = "open")
GDCdownload(query)
data <- GDCprepare(query)
data[grep("ENSG00000083093",data$`Gene Symbol`) ,-c(1:3)] %>% t %>% table

dim(data)

## [1] 19729   509

data[1:5,1:5]

## # A tibble: 5 x 5
##   `Gene Symbol`   `Gene ID` Cytoband `TCGA-A6-5664-01A-… `TCGA-AD-6548-01A…
##   <chr>               <dbl> <chr>                  <dbl>              <dbl>
## 1 ENSG0000000812…         0 1p36.33                    0                  0
## 2 ENSG0000000813…         0 1p36.33                    0                  0
## 3 ENSG0000006760…         0 1p36.33                    0                  0
## 4 ENSG0000007836…         0 1p36.33                    0                  0
## 5 ENSG0000007880…         0 1p36.33                    0                  0

data[grep("ENSG00000083093",data$`Gene Symbol`) ,-c(1:3)] %>% t %>% table

## .
##  -1   0   1 
##   4 494   8